Contacts of the helix formed by residues 87 - 107 (chain A) in PDB entry 5SY1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A HIS 4.5 4.7 + - - -
85A GLN 3.3 6.4 + - - +
86A HIS* 1.3 74.6 - - - +
88A GLY* 1.3 59.5 + - - +
89A LEU 3.5 2.5 - - - +
90A ALA* 4.4 4.0 - - - +
91A VAL* 3.3 26.1 + - + +
270A ARG* 3.9 29.1 - - - +
271A PHE* 4.5 19.8 + - - +
272A PRO 4.7 1.8 - - - -
273A LEU* 3.7 28.5 - - + +
276A ALA* 3.8 29.6 - - + -
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A HIS* 3.1 25.4 + - - -
87A LYS* 1.3 77.1 - - - +
89A LEU* 1.3 66.6 + - - +
91A VAL* 4.6 1.5 - - - +
92A ALA* 3.4 15.9 + - - +
195A PHE* 3.2 32.8 - - - -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 4.7 12.8 - - + -
86A HIS* 4.5 17.4 + - + +
87A LYS* 3.5 0.6 - - - +
88A GLY* 1.3 76.8 - - - +
90A ALA* 1.3 60.3 + - - +
92A ALA* 3.1 6.4 + - - +
93A VAL* 3.0 31.7 + - - +
139A LEU* 4.0 11.2 - - + +
142A GLY* 4.0 24.9 - - - +
150A TYR* 6.1 0.4 - - + -
195A PHE* 5.2 0.2 - - - -
196A LEU* 4.9 7.2 - - + -
199A GLN* 3.8 29.2 - - + +
200A TYR* 3.7 36.8 - - + +
203A LEU* 5.2 10.3 - - + -
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 5.1 9.2 - - + -
80A PHE* 5.2 2.5 - - + -
86A HIS 5.4 0.8 + - - +
87A LYS* 4.4 4.0 + - - +
89A LEU* 1.3 75.7 - - - +
91A VAL* 1.3 65.9 + - - +
93A VAL* 3.5 0.3 + - - -
94A TYR* 3.1 37.7 + - + -
139A LEU* 3.8 16.6 - - + -
273A LEU* 4.2 24.0 - - + -
277A ILE* 4.1 19.7 - - + -
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Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LYS* 3.3 33.1 + - + +
88A GLY* 4.6 1.6 - - - +
89A LEU 3.4 0.4 - - - -
90A ALA* 1.3 76.3 - - + +
92A ALA* 1.3 63.0 + - - +
94A TYR* 4.1 0.7 - - - +
95A GLY* 3.1 19.8 + - - -
192A CYS* 4.6 1.2 - - - -
276A ALA* 4.4 6.7 - - + +
277A ILE* 3.9 32.3 - - + +
280A VAL* 3.8 40.1 - - + +
281A VAL* 5.2 2.4 - - + +
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLY 3.4 18.1 + - - +
89A LEU 3.1 5.9 + - - +
91A VAL* 1.3 80.7 - - - +
93A VAL* 1.3 62.2 + - - +
95A GLY 3.2 0.5 + - - -
96A VAL* 3.1 21.0 + - - +
192A CYS* 3.2 36.8 - - - +
195A PHE* 4.2 13.2 - - + -
196A LEU* 4.2 15.5 - - + -
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Residues in contact with VAL 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.0 15.9 + - + +
90A ALA 4.3 0.9 - - - +
91A VAL 3.4 0.2 - - - -
92A ALA* 1.3 73.2 - - - +
94A TYR* 1.3 61.3 + - - +
96A VAL* 3.1 8.2 + - - +
97A LEU* 2.9 30.8 + - + +
135A TYR* 4.4 18.6 - - + +
138A LEU* 4.4 17.3 - - + -
139A LEU* 3.7 30.3 - - + +
196A LEU* 4.5 17.3 - - + -
200A TYR* 5.5 0.2 - - - +
494B TYR* 3.4 26.2 - - + +
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Residues in contact with TYR 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A PHE* 3.2 25.5 - + - -
90A ALA* 3.1 28.4 + - + +
91A VAL 4.4 0.9 - - - +
93A VAL* 1.3 76.1 - - - +
95A GLY* 1.3 56.8 + - - +
97A LEU* 3.9 5.2 - - + +
98A PHE* 3.0 31.4 + - - +
139A LEU* 5.0 3.8 - - + -
274A LYS* 5.2 4.3 - - + -
277A ILE* 3.7 44.6 - - + -
281A VAL* 4.0 10.3 - - + +
403A THR* 5.0 4.3 - - - -
493B SER 4.1 9.4 + - - -
494B TYR* 3.2 37.8 - + - -
497B PHE* 3.5 51.5 - + + -
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Residues in contact with GLY 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A VAL 3.1 17.2 + - - -
92A ALA 3.2 6.3 + - - -
93A VAL 3.2 0.2 - - - -
94A TYR* 1.3 76.2 - - - +
96A VAL* 1.3 59.6 + - - +
98A PHE* 4.3 2.3 - - - +
99A CYS* 3.3 26.3 + - - -
188A PRO* 5.4 0.3 - - - +
189A GLN* 5.3 0.3 - - - -
192A CYS* 4.4 7.9 - - - +
280A VAL* 5.9 0.9 - - - -
281A VAL* 4.4 6.2 - - - +
284A ILE* 3.7 26.0 - - - +
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Residues in contact with VAL 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA 3.1 14.3 + - - +
93A VAL* 3.1 10.6 + - - +
95A GLY* 1.3 77.4 - - - +
97A LEU* 1.3 64.7 + - - +
98A PHE 3.2 1.6 - - - -
99A CYS* 3.1 16.4 + - - +
100A LYS* 3.4 11.8 + - + +
135A TYR* 3.7 41.3 - - + +
189A GLN* 4.4 20.4 + - + +
192A CYS* 4.1 17.5 - - + -
193A LEU* 4.1 25.6 - - + +
196A LEU* 5.5 2.2 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A VAL* 2.9 22.6 + - + +
94A TYR* 3.4 6.0 + - - +
96A VAL* 1.3 75.6 - - - +
98A PHE* 1.3 61.0 + - - +
99A CYS 3.4 0.2 - - - -
100A LYS* 3.9 4.7 + - - +
101A LEU 3.8 5.4 + - - -
131A TYR* 3.5 44.4 - - + +
132A PRO* 3.6 15.7 - - + -
135A TYR* 4.0 13.0 - - + -
494B TYR* 3.3 39.5 - - + +
497B PHE* 4.3 19.7 - - + -
498B LEU* 3.4 25.6 - - + +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR 3.0 17.2 + - - +
95A GLY* 4.7 4.5 - - - +
96A VAL 3.2 0.2 - - - -
97A LEU* 1.3 78.1 - - - +
99A CYS* 1.3 63.9 + - - +
101A LEU* 3.1 37.6 + - + +
102A VAL* 3.4 27.9 + - + +
281A VAL* 4.2 21.8 - - + -
284A ILE* 3.9 21.1 - - + -
285A ALA* 3.6 37.5 - - + -
288A GLN* 4.8 0.9 - - + -
407A ALA* 4.3 14.6 - - + -
411A CYS* 4.4 12.6 - - - -
497B PHE* 4.5 6.0 - + + -
498B LEU* 4.5 4.3 - - + -
501B VAL* 4.7 17.5 - - + -
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Residues in contact with CYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLY 3.3 18.8 - - - -
96A VAL 3.1 8.5 + - - +
98A PHE* 1.3 79.7 - - - +
100A LYS* 1.3 62.0 + - - +
102A VAL* 3.1 20.1 + - - +
103A GLY* 3.2 10.2 + - - -
185A GLY 5.7 4.3 - - - +
188A PRO* 4.1 19.5 - - - -
189A GLN* 4.1 29.7 - - + +
284A ILE* 3.9 23.3 - - - -
288A GLN* 4.9 7.9 - - - +
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Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A VAL* 3.4 11.0 + - + +
97A LEU* 4.2 6.5 - - - +
98A PHE 3.3 0.6 - - - -
99A CYS* 1.3 77.2 - - - +
101A LEU* 1.3 60.6 - - - +
103A GLY* 4.1 2.3 - - - +
104A MET* 3.2 25.2 + - - +
131A TYR* 3.6 46.7 + - + -
135A TYR* 5.6 1.8 - - + -
189A GLN* 4.9 11.1 + - - +
498B LEU* 5.6 0.9 - - + -
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU 3.8 1.8 + - - -
98A PHE* 3.1 22.6 + - + +
100A LYS* 1.3 77.3 - - - +
102A VAL* 1.3 65.8 + - + +
104A MET* 3.3 22.5 + - + +
105A VAL* 3.4 23.3 + - + +
128A LEU* 3.8 28.9 - - + -
498B LEU* 3.9 31.3 - - + +
501B VAL* 3.7 33.4 - - + -
502B MET* 4.6 14.8 - - + -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 3.4 37.7 + - + +
99A CYS* 3.1 10.2 + - - +
101A LEU* 1.3 79.6 - - + +
103A GLY* 1.3 63.2 + - - +
104A MET 3.3 0.9 + - - -
105A VAL* 3.5 11.6 + - - +
106A LEU* 3.7 17.2 + - + +
181A TYR* 4.9 9.6 - - - +
288A GLN* 3.4 41.5 - - + +
292A LEU* 6.4 2.2 - - + -
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Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A CYS 3.2 9.2 + - - -
100A LYS* 4.1 2.7 - - - -
102A VAL* 1.3 80.5 - - - +
104A MET* 1.3 61.6 + - - +
106A LEU* 3.5 9.4 + - - +
107A SER* 3.5 23.9 + - - -
110A PRO* 5.1 0.2 - - - +
176A GLN* 5.3 0.3 + - - -
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Residues in contact with MET 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A LYS 3.2 18.8 + - - +
101A LEU* 3.7 15.3 - - + +
102A VAL 3.2 1.0 - - - -
103A GLY* 1.3 76.2 - - - +
105A VAL* 1.3 64.0 + - + +
106A LEU 3.3 0.2 - - - -
107A SER 2.9 20.1 - - - +
110A PRO* 4.0 22.3 - - + +
111A LEU* 5.8 1.3 - - + -
124A MET* 4.6 13.4 - - + +
127A ALA* 3.6 33.9 - - + +
128A LEU* 3.8 30.1 - - + -
131A TYR* 4.6 13.7 - - + +
498B LEU* 6.5 0.9 - - - -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 3.4 25.1 + - + +
102A VAL* 4.0 7.4 - - - +
103A GLY 3.3 0.6 - - - -
104A MET* 1.3 82.6 - - + +
106A LEU* 1.3 71.7 + - + +
107A SER 3.9 2.8 - - - +
108A HIS* 4.8 6.6 + - - -
502B MET* 5.7 7.6 - - + -
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A VAL* 3.7 20.4 - - + +
103A GLY* 3.5 9.1 + - - +
104A MET 3.3 0.4 - - - -
105A VAL* 1.3 85.5 - - + +
107A SER* 1.3 65.5 + - - +
108A HIS* 3.3 17.3 + - - -
176A GLN* 3.6 16.4 + - - +
177A ILE* 5.1 13.5 - - + -
181A TYR* 3.3 41.3 - - + +
292A LEU* 4.2 28.5 - - + -
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLY 3.5 10.4 + - - -
104A MET 2.9 20.3 - - - +
105A VAL 3.9 1.1 - - - +
106A LEU* 1.3 77.4 - - - +
108A HIS* 1.3 62.1 + - - +
109A HIS* 2.8 37.4 + - - -
110A PRO* 3.3 18.4 - - - +
124A MET* 5.7 0.2 - - - +
176A GLN* 3.4 17.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il