Contacts of the helix formed by residues 90 - 107 (chain A) in PDB entry 2WZJ
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 ASN 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLN 4.4 0.4 + - - -
89A LEU* 1.3 76.8 - - - +
91A SER* 1.3 56.8 + - - +
92A SER* 2.9 23.4 - - - +
93A SER* 2.8 55.3 + - - -
94A LEU* 3.0 11.0 + - - +
202A PHE 5.1 1.2 + - - -
204A ASN* 5.6 2.4 + - - -
225B LYS* 4.1 11.7 + - - +
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Residues in contact with SER 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU 4.1 0.8 + - - -
90A ASN* 1.3 70.9 - - - +
92A SER* 1.3 60.0 + - - +
94A LEU* 4.0 13.9 - - - +
95A GLN* 3.3 24.6 + - - +
170B PHE* 5.5 2.8 - - - -
228B GLY* 3.7 26.2 + - - -
229B PRO* 4.1 7.4 - - - +
230B GLU* 3.1 26.8 + - - -
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Residues in contact with SER 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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90A ASN* 2.8 17.6 + - - +
91A SER* 1.3 83.9 + - - +
93A SER* 1.3 62.1 + - - +
95A GLN* 3.5 4.7 + - - +
96A LYS* 3.4 18.7 + - - +
99A ARG* 5.3 0.7 + - - -
225B LYS* 3.5 23.3 - - - -
227B ASP* 2.7 37.2 + - - +
228B GLY 5.1 0.2 - - - +
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.3 10.5 - - - +
90A ASN* 2.8 33.7 + - - +
92A SER* 1.3 74.2 - - - +
94A LEU* 1.3 60.7 + - - +
96A LYS* 3.3 7.4 + - - +
97A LEU* 2.9 29.3 + - - +
202A PHE* 3.4 42.4 + - - +
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Residues in contact with LEU 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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86A LYS* 3.8 35.9 - - + +
89A LEU* 3.9 39.3 - - + +
90A ASN 3.0 9.8 + - - +
91A SER* 4.1 10.8 - - - +
93A SER* 1.3 76.0 - - - +
95A GLN* 1.3 65.0 + - - +
97A LEU* 3.3 12.9 + - + +
98A PHE* 3.0 38.4 + - + -
170B PHE* 3.9 30.5 - - + -
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Residues in contact with GLN 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 SER 3.3 17.0 + - - +
92A SER 3.6 4.4 + - - +
93A SER 3.2 0.2 - - - -
94A LEU* 1.3 81.6 - - - +
96A LYS* 1.3 55.4 + - - +
98A PHE* 3.4 2.1 + - - +
99A ARG* 2.9 57.1 + - - +
102A ARG* 4.4 3.6 + - - -
170B PHE* 3.3 34.7 - - + +
171B ILE* 5.0 0.3 - - - -
172B VAL* 3.8 18.0 + - + +
174B ARG* 2.8 41.5 + - - +
227B ASP* 3.5 17.0 + - - +
228B GLY* 5.5 0.9 - - - -
229B PRO* 6.0 0.4 - - + -
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Residues in contact with LYS 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 SER 3.4 8.9 + - - +
93A SER* 3.3 9.5 + - - +
94A LEU 3.3 0.6 - - - -
95A GLN* 1.3 76.2 - - - +
97A LEU* 1.3 66.7 + - - +
99A ARG* 2.9 30.7 + - - +
100A GLU* 2.8 58.7 + - - +
200A PHE* 4.2 22.9 - - + -
202A PHE* 4.7 9.4 - - + -
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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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84A ILE* 3.7 38.4 - - + -
86A LYS* 5.3 0.4 - - + -
89A LEU* 4.4 4.7 - - + -
93A SER 2.9 14.0 + - - +
94A LEU* 3.4 20.6 - - + +
96A LYS* 1.3 75.5 - - - +
98A PHE* 1.3 76.9 + - + +
100A GLU* 3.2 6.0 + - - +
101A VAL* 2.9 34.6 + - + +
125A LEU* 3.9 21.3 - - + -
127A LEU* 4.6 0.7 - - + -
196A PHE* 3.9 19.7 - - + -
202A PHE* 3.9 16.9 - - + -
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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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86A LYS* 5.1 4.0 - - + -
94A LEU* 3.0 28.4 + - + +
95A GLN 3.9 1.6 - - - +
97A LEU* 1.3 94.7 - - + +
99A ARG* 1.3 66.3 + - - +
100A GLU 3.0 1.8 - - - -
101A VAL* 3.2 12.3 + - + +
102A ARG* 2.9 35.3 + - - +
120A GLU* 3.9 27.1 - - - -
125A LEU* 4.2 18.8 - - + -
168B GLN 4.8 3.6 - - - -
169B LYS* 4.2 10.1 - - - +
170B PHE* 3.5 52.0 - + + -
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Residues in contact with ARG 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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92A SER 5.3 1.0 + - - -
95A GLN* 2.9 47.6 + - - +
96A LYS* 2.9 39.2 + - + +
98A PHE* 1.3 75.5 - - - +
100A GLU* 1.3 64.6 + - - +
102A ARG* 3.5 27.8 + - - +
103A ILE* 3.4 25.8 + - + +
99B ARG* 4.2 31.6 - - + +
174B ARG* 5.7 0.8 - - - +
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Residues in contact with GLU 100 (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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96A LYS* 2.8 56.2 + - - +
97A LEU* 3.6 8.3 - - - +
99A ARG* 1.3 81.4 + - - +
101A VAL* 1.3 60.6 + - - +
102A ARG 3.2 1.1 - - - -
103A ILE* 3.1 14.3 + - + +
104A MET* 2.9 26.5 + - - +
195A GLY* 2.9 32.5 - - - +
196A PHE* 3.6 22.5 + - + +
197A SER 5.1 0.9 + - - -
200A PHE* 5.2 2.9 - - - -
202A PHE* 4.5 9.0 - - - -
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Residues in contact with VAL 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* 2.9 27.5 + - + +
98A PHE* 3.8 13.9 - - + +
100A GLU* 1.3 75.2 - - - +
102A ARG* 1.3 65.1 + - - +
104A MET* 3.1 13.8 + - + +
105A LYS* 2.9 46.4 + - + +
115A LEU* 4.6 4.0 - - + -
118A VAL* 4.5 16.8 - - + -
125A LEU* 4.9 3.4 - - + -
127A LEU* 3.7 35.2 - - + -
196A PHE* 5.1 0.7 - - + -
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Residues in contact with ARG 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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95A GLN* 4.4 3.2 + - - -
98A PHE* 2.9 15.9 + - - +
99A ARG* 3.5 51.2 - - - +
101A VAL* 1.3 79.6 - - - +
103A ILE* 1.3 60.4 + - + +
105A LYS* 3.6 21.2 + - + +
106A VAL* 3.6 13.3 + - - +
99B ARG* 6.0 2.2 - - - +
102B ARG* 5.7 3.8 + - - -
103B ILE* 3.9 34.6 - - - +
106B VAL* 5.0 12.8 - - + -
169B LYS* 3.4 25.3 + - - +
170B PHE 3.9 13.1 + - - -
171B ILE* 4.0 17.9 - - - +
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Residues in contact with ILE 103 (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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99A ARG* 3.4 19.8 + - + +
100A GLU* 3.1 22.4 + - + +
102A ARG* 1.3 73.3 - - + +
104A MET* 1.3 67.9 + - - +
105A LYS 3.1 1.6 - - - -
106A VAL* 3.0 26.2 + - - +
107A LEU* 3.5 20.0 + - + +
171A ILE* 4.4 22.0 - - + -
194A PHE 4.3 4.3 - - - +
195A GLY* 3.6 22.2 - - - +
99B ARG* 4.8 17.3 - - + -
102B ARG* 4.4 17.9 - - - +
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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 GLU 2.9 6.8 + - - +
101A VAL* 3.1 23.3 + - + +
103A ILE* 1.3 79.9 - - - +
105A LYS* 1.3 61.3 + - - +
107A LEU* 3.5 21.4 + - + +
113A VAL* 5.0 12.6 - - - +
114A LYS* 5.8 0.7 + - - +
115A LEU* 4.0 31.6 + - + +
127A LEU* 4.6 2.2 - - + -
129A MET* 3.7 29.6 - - + +
195A GLY* 4.7 4.0 - - - +
196A PHE* 2.9 51.8 - - + +
351A TYR* 4.8 0.2 + - - -
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Residues in contact with LYS 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 VAL* 2.9 34.4 + - + +
102A ARG* 3.8 17.8 - - + +
103A ILE 3.1 0.6 + - - -
104A MET* 1.3 79.6 - - - +
106A VAL* 1.3 60.2 + - - +
107A LEU 3.3 2.3 + - - +
108A ASN* 5.8 0.7 - - - +
114A LYS* 4.5 3.8 + - - -
115A LEU* 3.6 11.0 - - + -
118A VAL* 4.3 14.1 - - - +
349A GLN* 4.7 6.6 + - - +
350A ARG 5.4 2.4 + - - -
351A TYR* 2.7 59.9 + - + +
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Residues in contact with VAL 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 ARG 3.6 8.2 + - - +
103A ILE* 3.0 21.4 + - - +
105A LYS* 1.3 77.6 - - + +
107A LEU* 1.3 70.4 + - + +
108A ASN* 3.7 5.1 + - - +
165A TYR* 3.7 9.0 + - - -
169A LYS* 4.1 15.4 - - + +
171A ILE* 4.4 10.5 - - + -
318A GLU* 5.0 1.6 - - - +
102B ARG* 4.1 30.5 - - + +
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Residues in contact with LEU 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 ILE* 3.5 25.3 + - + +
104A MET* 4.0 14.9 - - - +
105A LYS 3.3 4.9 - - - +
106A VAL* 1.3 82.0 - - + +
108A ASN* 1.3 59.5 + - - +
109A HIS 3.9 3.5 + - - -
112A ILE* 4.2 21.0 - - + +
113A VAL 5.4 1.7 - - - +
114A LYS* 4.4 19.4 - - - +
165A TYR* 3.8 18.2 - - + -
166A CYS* 3.9 20.9 - - - -
169A LYS* 4.2 5.4 - - + -
171A ILE* 4.2 19.7 - - + -
194A PHE* 3.8 32.1 - - + -
195A GLY 4.9 0.7 - - - +
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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