Contacts of the helix formed by residues 87 - 101 (chain A) in PDB entry 3X0X
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 ASP 87 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TRP* 4.9 0.9 - - + -
35A ALA* 4.3 8.6 - - - +
38A ARG* 2.7 42.5 + - - +
83A ILE 2.9 9.8 + - - +
84A ALA* 3.3 4.3 + - - -
86A ALA* 1.3 83.4 - - + +
88A GLY* 1.3 68.6 + - - +
89A SER* 3.1 23.6 + - - -
90A LEU* 3.1 28.5 + - + +
91A GLY 2.9 19.8 + - - -
212A GLN* 5.0 0.2 - - - +
384A ASN* 5.5 0.7 + - - -
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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
----------------------------------------------------------
84A ALA* 3.4 8.0 + - - -
87A ASP* 1.3 73.8 + - - +
89A SER* 1.3 56.8 + - - +
91A GLY* 3.5 0.7 + - - -
92A HIS* 2.9 29.1 + - - +
210A MET* 3.6 11.1 - - - +
261A VAL* 4.0 2.1 - - - +
265A ILE* 3.7 31.3 - - - +
384A ASN* 3.9 15.6 - - - +
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP* 3.1 11.4 + - - -
88A GLY* 1.3 74.5 - - - +
90A LEU* 1.3 62.2 + - - +
92A HIS* 3.4 3.3 + - - +
93A LEU* 2.9 29.0 + - - +
210A MET* 3.3 20.0 - - - -
211A ARG 3.3 2.1 + - - -
212A GLN* 3.2 42.8 + - - +
213A THR* 3.7 15.5 - - - +
384A ASN* 4.4 5.8 + - - +
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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
----------------------------------------------------------
31A TRP* 3.6 38.4 - - + -
38A ARG* 4.0 2.9 - - - +
45A ALA* 3.8 17.7 - - + +
48A GLU* 3.7 35.9 - - + +
49A ARG* 5.0 0.7 - - + +
52A LEU* 5.2 6.1 - - + +
83A ILE* 3.6 15.0 - - + -
87A ASP* 3.1 30.8 + - + +
89A SER* 1.3 77.9 - - - +
91A GLY* 1.3 55.7 + - - +
93A LEU* 3.5 17.1 - - + +
94A PHE* 2.7 38.3 + - - +
212A GLN* 5.4 1.1 - - - +
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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
----------------------------------------------------------
80A VAL* 4.1 5.2 - - - +
83A ILE* 3.4 18.0 - - - +
84A ALA* 3.8 18.6 - - - -
87A ASP 2.9 18.8 + - - -
88A GLY 3.9 0.4 - - - -
90A LEU* 1.3 70.2 - - - +
92A HIS* 1.3 58.3 + - - +
94A PHE* 3.8 2.0 - - - +
95A GLY* 2.8 29.1 + - - -
261A VAL* 4.0 10.0 - - - +
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Residues in contact with HIS 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLY 2.9 18.9 + - - +
89A SER 3.6 3.8 - - - +
91A GLY* 1.3 75.8 - - - +
93A LEU* 1.3 59.4 + - - +
96A TYR* 2.9 61.1 + + + +
163A SER* 4.7 5.2 - - - -
210A MET* 4.0 15.3 - - + -
213A THR* 3.4 25.1 + - + +
215A SER* 4.1 17.9 - - - -
258A PHE* 4.5 7.6 - + - -
261A VAL* 4.1 14.4 - - + +
388A HIS* 3.6 37.8 + + - -
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Residues in contact with LEU 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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45A ALA* 5.8 0.2 - - + -
49A ARG* 3.6 43.7 - - + +
89A SER 2.9 17.6 + - - +
90A LEU* 3.1 15.5 + - + +
92A HIS* 1.3 78.7 - - + +
94A PHE* 1.3 66.9 + - - +
96A TYR* 4.0 2.6 - - - +
97A HIS* 3.0 24.6 + - - +
126A TRP* 3.7 29.6 - - + -
163A SER 5.5 0.2 - - - -
164A GLY* 4.1 13.5 - - - +
212A GLN 4.6 6.1 - - - +
213A THR* 3.5 30.7 - - - +
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Residues in contact with PHE 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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52A LEU* 3.8 24.5 - - + -
57A LEU* 3.5 39.9 - - + -
58A LEU* 3.8 22.4 - - + -
60A LEU* 4.3 5.4 - - + -
79A VAL* 3.6 22.2 - - + -
80A VAL* 4.1 13.2 - - + -
83A ILE* 3.5 21.5 - - + -
90A LEU 2.7 20.8 + - - +
91A GLY 3.9 2.0 - - - +
93A LEU* 1.3 76.4 - - - +
95A GLY* 1.3 63.2 + - - +
97A HIS* 3.3 12.4 + + - +
98A LEU* 3.1 44.6 + - + +
126A TRP* 4.3 5.8 - - - -
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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
----------------------------------------------------------
80A VAL* 3.9 18.6 - - - -
91A GLY 2.8 21.5 + - - -
92A HIS* 4.0 0.4 - - - -
94A PHE* 1.3 74.1 - - - +
96A TYR* 1.3 62.9 + - - +
98A LEU* 3.2 16.8 + - - +
99A THR* 3.5 11.8 + - - +
257A ILE* 3.6 23.9 - - - +
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Residues in contact with TYR 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 HIS* 2.9 46.3 + + + +
93A LEU* 4.0 3.4 - - - +
95A GLY* 1.3 75.6 - - - +
97A HIS* 1.3 66.0 + - - +
99A THR* 2.5 49.1 + - + -
100A ASN* 3.6 5.6 + - - -
129A ASN* 3.4 25.4 + - - -
131A SER* 5.2 1.7 + - - -
134A ASN* 5.7 0.5 + - - -
163A SER* 3.0 35.6 + - - +
250A PHE* 5.6 9.0 - + - -
254A ALA* 5.6 4.5 - - + -
257A ILE* 4.4 2.5 - - - +
258A PHE* 4.0 27.8 - + + -
388A HIS* 5.2 1.1 - - - -
391A HIS* 4.3 14.1 + + - -
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Residues in contact with HIS 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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58A LEU* 2.8 44.1 + - + -
93A LEU 3.0 14.7 + - - +
94A PHE* 3.3 15.0 - + - +
96A TYR* 1.3 74.5 - - - +
98A LEU* 1.3 77.3 + - + +
100A ASN* 3.1 19.1 + - - +
101A ALA* 4.3 2.4 + - - +
120A ILE* 5.1 2.5 - - + -
125A TRP 3.6 16.8 - - - -
126A TRP* 3.9 20.1 - + + -
127A THR* 3.0 65.3 + - + +
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Residues in contact with LEU 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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58A LEU 4.5 3.1 - - - +
60A LEU* 4.2 16.4 - - + -
61A LEU* 3.8 35.2 - - + +
73A TRP* 5.5 0.7 - - + -
76A ALA* 4.4 14.4 - - + +
80A VAL* 3.7 30.1 - - + -
94A PHE* 3.1 36.7 + - + +
95A GLY* 3.4 8.3 - - - +
96A TYR 3.0 1.2 - - - -
97A HIS* 1.3 91.3 - - + +
99A THR* 1.3 62.6 + - + +
101A ALA* 5.3 0.4 - - - +
102A PRO* 3.1 23.1 - - - +
257A ILE* 4.8 7.6 - - + -
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Residues in contact with THR 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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73A TRP* 5.5 0.7 - - + -
95A GLY 3.5 14.8 - - - +
96A TYR* 2.5 41.8 + - + +
98A LEU* 1.3 76.1 - - - +
100A ASN* 1.3 69.1 + - - +
102A PRO* 3.4 11.9 - - - +
103A MET* 3.9 8.8 + - - +
250A PHE* 6.2 1.5 - - - -
253A ILE* 4.0 27.6 - - + +
254A ALA* 4.2 20.2 - - + -
257A ILE* 4.2 11.2 - - + -
258A PHE* 6.1 0.7 - - + -
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Residues in contact with ASN 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 TYR 3.6 9.2 + - - -
97A HIS* 3.1 11.3 + - - +
99A THR* 1.3 79.7 + - - +
101A ALA* 1.3 55.0 + - - +
103A MET* 2.8 43.4 + - - +
127A THR* 3.0 42.4 + - - +
128A GLY* 3.7 14.6 - - - -
129A ASN* 3.0 31.2 + - - +
163A SER 5.3 0.4 + - - -
172A PHE* 3.6 23.1 - - + +
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Residues in contact with ALA 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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62A VAL* 5.0 7.4 - - + -
97A HIS 4.3 2.9 + - - +
98A LEU 5.3 0.2 - - - +
100A ASN* 1.3 75.4 - - - +
102A PRO* 1.4 61.5 - - + +
104A ILE* 2.7 44.9 + - + +
117A TYR* 3.5 23.9 + - + -
120A ILE* 3.8 22.9 - - + -
127A THR* 4.7 4.4 + - + -
172A PHE* 3.9 4.2 - - - -
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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