Contacts of the helix formed by residues 87 - 94 (chain A) in PDB entry 2WA2
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 SER 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A SER* 2.8 32.5 + - - -
60A THR* 3.4 20.1 + - - -
85A ARG* 3.7 4.8 - - - +
86A GLY* 1.3 75.3 - - - +
88A TRP* 1.3 57.3 + - - +
90A TYR* 3.4 8.1 + - - +
91A TYR* 2.9 28.2 + - - +
1248A SAM 3.0 23.8 + - - -
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Residues in contact with TRP 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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59A GLY* 3.0 32.2 + - - -
62A LYS* 4.9 3.7 - - + +
63A LEU* 3.6 35.6 - - + +
66A ILE* 5.2 2.0 - - + -
80A ASP* 3.5 17.7 - - - +
86A GLY 3.3 0.2 - - - -
87A SER* 1.3 79.4 - - - +
89A SER* 1.3 59.1 + - - +
91A TYR* 3.3 2.5 + - - +
92A ALA* 2.8 30.5 + - - +
145A LEU* 3.8 24.6 - - + +
146A CYS 3.8 9.4 - - - -
147A ASP* 3.5 37.1 + - + -
182A CYS* 3.8 30.7 - - - -
222A TYR* 3.5 34.3 - + - -
1248A SAM 3.3 26.7 + - - +
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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
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80A ASP* 2.6 27.4 + - - +
86A GLY 3.1 10.4 + - - -
88A TRP* 1.3 77.7 - - - +
90A TYR* 1.3 52.0 + - - +
92A ALA* 3.4 2.5 + - - +
93A ALA* 2.8 35.5 + - - +
101A VAL* 3.6 16.9 - - - +
103A ALA* 3.2 19.6 - - - +
125A ILE* 3.6 8.0 - - - +
127A PHE* 3.9 21.2 - - - -
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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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85A ARG 4.6 2.2 - - - -
86A GLY 3.1 27.6 + - - +
87A SER* 3.9 6.3 - - - +
89A SER* 1.3 73.1 - - - +
91A TYR* 1.3 68.4 + - - +
93A ALA* 3.5 2.3 + - + +
94A SER* 3.4 20.1 + - - -
115A ARG 3.3 18.6 - - - -
116A LEU* 3.2 12.3 - - - +
117A VAL* 2.9 48.5 + - + -
119A THR* 3.7 19.9 + - - +
120A PHE 4.6 4.8 - - - +
122A TRP* 3.9 16.2 - - + +
125A ILE* 3.5 18.6 - - + -
127A PHE* 3.5 28.5 - + - -
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Residues in contact with TYR 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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60A THR* 4.2 25.1 + - + -
63A LEU* 3.6 28.0 - - + -
64A ALA* 3.7 23.4 - - + -
67A ASP* 2.7 31.1 + - + +
68A GLU* 3.7 15.8 + - - -
74A LEU* 3.5 22.9 - - + -
87A SER 2.9 18.4 + - - +
88A TRP* 3.6 5.2 - - - +
90A TYR* 1.3 76.7 - - - +
92A ALA* 1.3 62.1 + - - +
94A SER* 2.7 25.5 + - - -
95A GLN* 3.5 25.9 + - + +
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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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63A LEU* 5.1 0.2 - - + -
74A LEU* 4.4 13.0 - - + -
78A VAL* 4.2 23.8 - - + -
88A TRP 2.8 20.4 + - - +
89A SER* 3.7 6.1 - - - +
91A TYR* 1.3 78.8 - - - +
93A ALA* 1.3 57.8 + - - +
95A GLN* 3.1 17.2 + - - +
98A VAL* 3.2 21.6 - - + +
101A VAL* 4.1 12.3 - - + -
145A LEU* 4.4 8.1 - - + -
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Residues in contact with ALA 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 SER 2.8 20.7 + - - +
90A TYR* 4.0 4.3 - - - +
91A TYR 3.2 0.2 - - - -
92A ALA* 1.3 72.7 - - - +
94A SER* 1.3 58.1 + - - +
95A GLN 3.3 3.4 + - - +
98A VAL* 4.5 3.6 - - - -
101A VAL* 3.9 10.3 - - + +
120A PHE* 4.9 2.6 - - - -
121A GLY* 3.3 40.2 - - - +
124A LEU* 3.7 18.3 - - + +
125A ILE* 3.5 19.7 - - + -
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Residues in contact with SER 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 3.4 10.9 + - - -
91A TYR* 2.7 24.0 + - - -
93A ALA* 1.3 79.1 - - - +
95A GLN* 1.3 73.5 + - - +
96A PRO* 4.0 2.3 - - - +
120A PHE* 4.0 39.6 - - - -
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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