Contacts of the helix formed by residues 87 - 102 (chain A) in PDB entry 4DHZ
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 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ASP* 3.1 28.5 + - - +
86A GLY* 1.3 79.7 - - - +
88A CYS* 1.3 65.2 + - - +
89A PHE 3.3 2.2 - - - -
90A TYR* 3.1 8.3 + - - -
91A ARG* 3.0 26.4 + - - +
170A LEU* 3.8 17.5 - - + -
174A ARG* 2.8 30.0 + - - +
209A MET* 3.4 20.7 - - - +
210A TRP* 2.8 38.3 + - - -
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Residues in contact with CYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 3.8 12.2 - - + +
83A ARG 4.0 8.3 - - - +
85A ASP* 3.8 1.6 + - - -
87A ASN* 1.3 76.5 - - - +
89A PHE* 1.3 61.3 + - - +
91A ARG* 3.1 1.0 + - - +
92A ALA* 2.7 38.4 + - - +
267A HIS* 3.9 11.0 - - + -
268A TYR* 3.8 33.4 - - - +
575B GLY 3.6 2.0 + - - -
576B GLZ 1.8 59.1 + - - +
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Residues in contact with PHE 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASN 3.3 0.8 - - - -
88A CYS* 1.3 81.9 - - - +
90A TYR* 1.3 72.1 + + + +
92A ALA* 3.3 5.3 + - - +
93A ILE* 3.0 45.3 + - + +
213A ALA* 3.8 31.0 - - + -
217A ALA 4.7 0.7 - - - -
218A ILE* 3.6 54.7 - - + -
221A LEU* 3.5 25.8 - - + -
222A ILE* 4.4 4.5 - - + -
231A ILE* 5.1 2.9 - - + -
261A LEU* 3.9 21.8 - - + -
268A TYR* 3.7 25.1 - + + -
575B GLY 4.6 2.6 + - - +
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Residues in contact with TYR 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 GLY 5.1 0.4 - - - -
87A ASN* 3.1 10.1 + - - +
89A PHE* 1.3 81.4 - + + +
91A ARG* 1.3 65.0 + - - +
93A ILE* 3.2 3.6 + - - +
94A LEU* 3.0 27.2 + - - +
170A LEU* 3.8 17.7 - - + -
173A PHE* 4.3 10.5 - - + +
174A ARG* 3.4 56.6 + - + -
177A THR* 3.4 26.0 - - + -
205A GLU 5.1 0.5 + - - -
206A ILE* 4.0 16.7 - - + +
211A LYS 4.2 4.0 + - - -
212A ASP 5.2 0.3 + - - -
213A ALA* 3.9 22.6 - - + +
217A ALA* 3.6 22.6 - - + +
221A LEU* 3.7 24.1 - - + +
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Residues in contact with ARG 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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43A LEU* 3.5 48.3 - - - +
44A VAL* 4.1 13.9 - - + -
82A ILE* 3.9 12.5 - - + +
83A ARG 5.1 1.0 + - - -
85A ASP* 3.3 27.9 + - - -
87A ASN* 3.0 24.1 + - - +
88A CYS 3.6 5.4 - - - +
90A TYR* 1.3 75.5 - - - +
92A ALA* 1.3 61.7 + - - +
94A LEU* 3.4 16.5 + - + +
95A VAL* 3.1 29.5 + - + +
160A LEU* 5.5 1.1 - - + +
166A ALA* 3.5 27.5 + - - +
167A ASN* 2.8 30.3 + - - -
170A LEU* 3.6 19.8 - - + +
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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
----------------------------------------------------------
82A ILE* 4.2 13.1 - - + +
88A CYS 2.7 22.1 + - - +
89A PHE* 3.5 7.6 - - - +
91A ARG* 1.3 74.3 - - - +
93A ILE* 1.3 62.6 + - - +
95A VAL* 3.4 0.7 + - - +
96A GLY* 3.1 18.0 + - - -
261A LEU* 4.0 20.6 - - + +
268A TYR* 4.5 8.5 - - + +
269A ASP 4.9 0.9 - - - -
270A VAL* 3.5 31.2 - - + +
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PHE* 3.0 48.2 + - + +
90A TYR 3.7 7.2 - - - +
92A ALA* 1.3 74.3 - - - +
94A LEU* 1.3 61.1 + - - +
96A GLY* 3.0 4.0 + - - -
97A LEU* 2.8 48.5 + - + +
173A PHE* 4.9 2.7 - - + -
221A LEU* 3.8 23.3 - - + -
222A ILE* 4.4 8.7 - - + -
225A ALA* 5.3 0.4 - - + -
227A THR* 5.2 6.3 - - + -
229A VAL* 4.0 26.9 - - + -
259A ILE* 4.0 8.0 - - + +
261A LEU* 4.3 12.6 - - + -
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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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90A TYR 3.0 19.1 + - - +
91A ARG* 3.4 22.4 - - + +
93A ILE* 1.3 79.3 - - - +
95A VAL* 1.3 62.2 + - + +
97A LEU* 3.7 6.0 - - - +
98A ILE* 2.9 43.8 + - + +
160A LEU* 3.4 33.2 - - + -
166A ALA 5.2 2.2 - - - +
169A ILE* 4.4 9.4 - - + -
170A LEU* 4.1 33.7 - - + +
173A PHE* 4.0 29.4 - - + -
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Residues in contact with VAL 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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44A VAL* 3.7 35.0 - - + -
80A ARG* 3.8 19.1 - - - -
82A ILE* 4.5 2.7 - - + -
91A ARG 3.1 21.1 + - - +
92A ALA 3.8 4.0 - - - +
94A LEU* 1.3 80.1 - - + +
96A GLY* 1.3 65.1 + - - +
98A ILE* 3.3 5.1 + - - +
99A GLU* 3.0 48.6 + - + +
157A TYR* 4.5 7.4 - - + -
160A LEU* 4.2 13.7 - - + -
270A VAL* 4.7 6.7 - - + -
272A TYR* 4.4 1.6 - - - +
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Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 3.1 9.8 + - - -
93A ILE 3.0 7.4 + - - -
95A VAL* 1.3 78.4 - - - +
97A LEU* 1.3 63.0 + - - +
99A GLU* 3.5 14.5 + - - +
100A ILE* 3.3 22.9 + - - +
259A ILE* 3.7 29.8 - - - -
270A VAL* 5.0 2.8 - - - +
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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
----------------------------------------------------------
93A ILE* 2.8 35.0 + - + +
94A LEU* 3.7 3.6 - - - +
96A GLY* 1.3 68.7 - - - +
98A ILE* 1.3 70.8 + - + +
100A ILE* 2.9 23.9 + - + +
101A MET* 3.0 27.6 + - + +
107A ARG* 5.0 7.9 - - - +
111A PHE* 4.4 12.6 - - + -
173A PHE* 3.6 31.0 - - + -
225A ALA* 4.1 19.1 - - + +
227A THR* 3.8 30.3 - - + +
259A ILE* 3.7 5.1 - - + +
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Residues in contact with ILE 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 LEU* 2.9 49.4 + - + +
95A VAL* 3.8 4.7 - - - +
97A LEU* 1.3 71.2 - - + +
99A GLU* 1.3 64.1 + - - +
101A MET* 3.1 32.4 + - + +
102A LEU* 3.1 33.7 + - + +
139A PHE* 4.7 11.2 - - + -
142A PHE* 3.9 32.3 - - + -
146A ILE* 4.9 4.9 - - + -
156A VAL* 3.8 18.2 - - + -
157A TYR* 4.8 6.3 - - + -
160A LEU* 4.4 9.6 - - + -
169A ILE* 5.3 0.2 - - + -
173A PHE* 5.3 1.6 - - + -
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Residues in contact with GLU 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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80A ARG* 2.9 26.0 + - - +
95A VAL* 3.0 26.1 + - + +
96A GLY* 3.6 13.9 - - - +
98A ILE* 1.3 73.8 - - - +
100A ILE* 1.3 66.8 + - + +
102A LEU* 3.3 13.2 + - - +
103A LYS* 3.3 25.2 + - - +
157A TYR* 2.9 20.6 + - + +
270A VAL* 4.8 0.3 - - - +
272A TYR* 2.4 43.4 + - - -
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Residues in contact with ILE 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 GLY 3.3 15.9 + - - +
97A LEU* 2.9 15.5 + - + +
99A GLU* 1.3 79.9 - - + +
101A MET* 1.3 59.4 + - + +
103A LYS* 3.0 10.0 + - - +
104A ASP* 2.9 29.7 + - + +
107A ARG* 3.9 35.9 - - + +
258A GLU* 3.3 50.0 - - + +
259A ILE* 3.8 10.5 - - + -
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Residues in contact with MET 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* 3.0 19.5 + - + +
98A ILE* 3.1 37.7 + - + +
100A ILE* 1.3 77.2 - - + +
102A LEU* 1.3 59.5 + - + +
103A LYS 3.3 1.6 - - - -
104A ASP 3.3 20.4 - - - +
105A ARG* 4.6 1.0 + - - -
107A ARG* 4.4 10.8 - - + -
108A LEU* 3.6 50.0 - - + +
111A PHE* 3.8 40.6 - - + -
139A PHE* 5.1 0.7 - - + -
143A LEU* 3.7 22.0 - - + -
146A ILE* 5.9 1.8 - - + -
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Residues in contact with LEU 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 ILE* 3.1 37.8 + - + +
99A GLU* 3.7 10.3 - - - +
100A ILE 3.1 0.6 - - - -
101A MET* 1.3 77.8 - - - +
103A LYS* 1.3 73.0 + - - +
104A ASP 5.2 0.4 - - - -
146A ILE* 3.5 31.2 - - + -
151A HIS 5.7 0.2 - - - +
152A THR 4.9 2.0 - - - +
153A GLU* 4.6 32.5 - - + +
156A VAL* 4.6 16.8 - - + -
157A TYR* 4.8 7.2 - - + +
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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
------------------------------------------------------------
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