Contacts of the helix formed by residues 78 - 98 (chain A) in PDB entry 5UAK
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 PHE 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 2.8 45.5 + - + +
75A ARG* 4.5 7.5 + - - +
76A CYS 3.6 3.0 + - - -
77A PHE* 1.3 74.2 - - - +
79A TRP* 1.3 87.1 + + + +
81A PHE* 3.5 6.0 - + - +
82A MET* 3.3 57.7 + - + +
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Residues in contact with TRP 79 (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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76A CYS 5.4 0.8 + - - -
77A PHE 3.6 0.2 - - - -
78A PHE* 1.3 97.9 - + + +
80A ARG* 1.3 87.4 + - + +
81A PHE 3.2 1.6 - - - -
82A MET* 3.0 14.6 + - + +
83A PHE* 2.8 28.7 + + + +
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Residues in contact with ARG 80 (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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77A PHE* 5.0 3.3 + - - +
78A PHE 4.9 0.4 - - - +
79A TRP* 1.3 103.1 - - + +
81A PHE* 1.3 56.5 + - - +
83A PHE* 3.4 34.5 - - - +
84A TYR* 2.8 54.5 + - + -
148A ILE* 4.2 5.8 - - + -
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Residues in contact with PHE 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.6 28.9 - - - -
77A PHE 3.4 23.6 + - - +
78A PHE* 3.5 9.8 - + - +
80A ARG* 1.3 78.6 - - - +
82A MET* 1.3 66.8 + - + +
84A TYR* 3.8 2.3 - - - +
85A GLY* 2.8 30.1 + - - -
145A LEU* 3.4 30.1 - - + +
148A ILE* 3.7 20.1 - - + +
195A LEU* 4.0 32.8 - - + -
198A ALA* 5.4 3.4 - - + -
199A HIS* 3.7 35.7 - + + -
361A TRP* 6.5 0.9 - + - -
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Residues in contact with MET 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.5 50.5 - - + +
79A TRP* 3.0 16.1 + - + +
81A PHE* 1.3 87.2 - - + +
83A PHE* 1.3 60.5 + - - +
85A GLY* 3.4 2.2 - - - +
86A ILE* 3.0 39.4 + - + +
199A HIS* 4.8 12.3 - - + +
202A TRP* 5.4 12.3 - - + +
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 2.8 20.3 + - + +
80A ARG* 3.3 43.7 + - - +
82A MET* 1.3 71.9 - - - +
84A TYR* 1.3 73.5 + + - +
86A ILE* 3.4 14.4 - - + +
87A PHE* 3.3 40.0 - + - -
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Residues in contact with TYR 84 (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 ARG* 2.8 39.9 + - + +
81A PHE 3.9 3.1 - - - +
83A PHE* 1.3 83.2 - + - +
85A GLY* 1.3 66.3 + - - +
87A PHE* 3.4 16.3 + + - +
88A LEU* 4.6 0.9 - - - +
140A PRO* 4.4 12.6 - - + -
141A ALA* 3.6 33.8 - - - +
144A GLY* 3.6 33.0 - - - -
145A LEU* 4.5 9.2 - - + -
147A HIS* 4.9 10.4 + - - -
148A ILE* 3.6 21.3 - - + -
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Residues in contact with GLY 85 (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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81A PHE 2.8 18.0 + - - -
82A MET 3.1 3.0 + - - -
84A TYR* 1.3 72.4 - - - +
86A ILE* 1.3 57.2 + - - +
88A LEU* 2.9 32.8 + - - +
89A TYR 3.5 2.1 + - - -
145A LEU* 5.0 2.2 - - - +
199A HIS* 3.2 39.8 - - - -
202A TRP* 5.2 0.2 - - - -
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Residues in contact with ILE 86 (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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82A MET* 3.0 24.1 + - + +
83A PHE* 3.4 19.5 - - + +
85A GLY* 1.3 71.4 - - - +
87A PHE* 1.3 94.4 + - + +
89A TYR* 3.1 12.7 + - + +
90A LEU* 2.8 33.4 + - + +
199A HIS* 5.3 0.2 - - - -
202A TRP* 5.3 10.7 - - + -
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Residues in contact with PHE 87 (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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83A PHE* 3.3 49.6 - + - -
84A TYR* 3.4 10.0 + + - +
85A GLY 3.2 0.8 - - - -
86A ILE* 1.3 92.2 - - + +
88A LEU* 1.3 61.2 + - - +
90A LEU* 3.6 15.0 + - + +
91A GLY* 3.3 17.0 + - - -
137A LEU* 4.0 38.2 - - + +
138A LEU* 4.4 2.1 - - - +
141A ALA* 3.6 24.0 - - + -
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Residues in contact with LEU 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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84A TYR 4.6 0.9 - - - +
85A GLY* 2.9 10.7 + - - +
87A PHE* 1.3 75.8 - - - +
89A TYR* 1.3 60.0 + - - +
91A GLY* 3.1 2.6 + - - -
92A GLU* 2.8 36.2 + - + +
138A LEU* 3.9 24.2 - - + +
141A ALA* 4.0 20.4 - - + -
142A ILE* 4.5 20.0 - - + +
145A LEU* 3.5 28.5 - - + -
196A ALA 4.6 0.9 - - - +
199A HIS* 4.0 22.2 - - + +
200A PHE* 4.3 28.9 - - + -
203A ILE* 5.2 1.6 - - + -
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Residues in contact with TYR 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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85A GLY 3.5 1.8 + - - -
86A ILE* 3.1 13.3 + - + +
88A LEU* 1.3 77.8 - - - +
90A LEU* 1.3 64.1 + - + +
92A GLU* 4.5 3.1 - - - -
93A VAL* 3.3 51.7 + - + +
202A TRP* 3.7 19.7 - + + -
203A ILE* 3.6 37.3 - - + +
206A LEU* 3.5 47.5 + - + +
207A GLN* 5.3 0.4 - - - -
210A LEU* 5.5 3.5 - - - +
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Residues in contact with LEU 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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86A ILE* 2.8 20.2 + - + +
87A PHE* 3.7 20.2 - - + +
88A LEU 3.2 0.2 - - - -
89A TYR* 1.3 81.1 - - + +
91A GLY* 1.3 57.1 + - - +
93A VAL* 3.5 10.1 - - + +
94A THR* 3.3 26.6 - - + +
137A LEU* 3.5 29.5 - - + +
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Residues in contact with GLY 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 PHE 3.3 10.0 + - - -
88A LEU 3.1 5.6 + - - -
90A LEU* 1.3 74.4 - - - +
92A GLU* 1.3 64.0 + - - +
93A VAL 3.2 2.0 - - - -
94A THR* 2.5 26.2 + - - -
95A LYS* 3.3 7.8 + - - -
134A ARG* 3.3 24.4 - - - -
137A LEU* 4.0 7.1 - - - +
138A LEU* 4.3 6.1 - - - -
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Residues in contact with GLU 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 LEU* 2.8 27.5 + - + +
89A TYR 4.3 2.5 - - - +
91A GLY* 1.3 72.3 - - - +
93A VAL* 1.3 56.2 - - + +
95A LYS* 3.6 38.6 + - - +
138A LEU* 4.7 4.5 - - + +
200A PHE* 3.3 15.6 - - + -
203A ILE* 3.9 26.7 - - + -
207A GLN* 2.8 37.4 + - - +
353A GLN* 3.1 33.5 + - - +
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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 TYR* 3.3 53.5 + - + +
90A LEU* 3.5 16.2 - - + +
92A GLU* 1.3 75.6 - - - +
94A THR* 1.3 66.2 + - + +
96A ALA* 2.8 24.3 + - - +
97A VAL* 2.9 17.7 + - + +
206A LEU 5.8 1.8 - - - +
207A GLN* 3.7 12.1 - - - +
210A LEU* 4.2 22.3 - - + +
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Residues in contact with THR 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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90A LEU* 3.3 17.7 - - + +
91A GLY* 2.5 27.7 + - - -
93A VAL* 1.3 77.3 - - + +
95A LYS* 1.3 59.0 + - - +
96A ALA 3.3 0.2 - - - -
97A VAL* 3.7 13.5 - - + +
98A GLN* 2.9 28.1 + - - +
130A LEU* 3.8 31.0 - - + +
133A VAL* 6.1 2.0 - - + +
134A ARG* 3.4 16.8 + - - +
137A LEU* 5.5 2.3 - - + +
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Residues in contact with LYS 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 GLY 3.3 4.0 + - - +
92A GLU* 3.6 43.2 + - - +
93A VAL 3.2 0.2 - - - -
94A THR* 1.3 77.6 + - - +
96A ALA* 1.3 57.3 + - - +
98A GLN* 3.2 28.2 - - - +
99A PRO* 3.6 6.6 - - - +
134A ARG* 3.5 31.3 - - - +
138A LEU* 3.7 25.9 - - - +
345A VAL* 4.4 26.7 - - + +
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Residues in contact with ALA 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 GLU 3.9 0.8 + - - -
93A VAL* 2.8 18.3 + - - +
95A LYS* 1.3 73.7 - - - +
97A VAL* 1.3 56.6 + - - -
99A PRO* 3.2 15.8 - - - +
100A LEU* 4.2 0.7 - - - +
207A GLN* 3.7 20.4 - - - +
210A LEU* 4.3 9.4 - - + -
211A LEU* 3.9 15.3 - - + -
214A LEU* 3.3 35.0 - - + +
342A PHE* 3.5 5.4 - - - +
345A VAL* 4.7 4.0 - - + -
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Residues in contact with VAL 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 25.6 + - + +
94A THR* 3.5 14.1 + - + +
96A ALA* 1.3 75.9 - - - +
98A GLN* 1.3 67.1 + - - +
99A PRO* 3.3 1.3 - - - -
100A LEU* 3.4 31.8 + - + +
101A LEU* 4.6 8.3 + - + +
130A LEU* 5.9 5.6 - - + -
210A LEU* 5.1 13.2 - - + -
214A LEU* 5.4 1.1 - - + -
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Residues in contact with GLN 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 THR 2.9 13.4 + - - +
95A LYS* 3.2 19.3 - - - +
97A VAL* 1.3 76.3 - - - +
99A PRO* 1.4 63.0 - - + +
100A LEU 3.2 5.0 + - - -
101A LEU* 3.5 10.9 + - - +
127A LEU* 3.7 25.8 - - + +
130A LEU* 5.7 11.0 - - + +
131A PHE* 3.2 44.8 - - + -
134A ARG* 3.8 18.1 + - - +
341A SER* 6.3 0.8 - - - -
1137A MET* 3.9 30.8 + - - +
1140A MET* 5.2 0.2 - - - +
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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