Contacts of the strand formed by residues 32 - 40 (chain P) in PDB entry 2A3W
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 32 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30P LEU* 3.6 10.0 - - - +
31P GLN* 1.3 99.4 - - - +
33P PHE* 1.3 64.2 - - - +
98P TRP* 3.5 5.2 - - - -
99P GLU* 3.4 26.5 - - - +
100P SER* 3.9 1.0 + - - -
101P SER* 5.0 1.6 + - - -
161P ASP* 3.1 25.7 + - - +
162P SER* 3.8 19.1 - - - +
163P VAL* 4.0 11.2 - - + -
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Residues in contact with PHE 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30P LEU* 4.4 11.9 - - + -
32P ASN* 1.3 77.7 - - - +
34P THR* 1.3 70.4 + - - +
35P LEU* 4.2 9.9 - - + -
61P LEU* 3.5 41.7 - - + -
73P LEU* 4.2 7.9 - - + -
75P ILE* 3.7 15.5 - - + -
96P VAL* 3.8 20.6 - - + -
97P SER* 3.2 4.7 - - - -
98P TRP* 3.1 68.2 + + + +
125P VAL* 4.8 3.4 - - + -
159P MET* 3.9 20.9 - - + -
160P TRP 3.2 13.5 - - - +
162P SER 3.2 10.0 + - - +
163P VAL* 4.5 0.2 - - - -
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Residues in contact with THR 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P PHE* 1.3 73.8 + - - +
35P LEU* 1.3 62.1 + - - +
36P CYS* 4.2 6.5 - - - -
96P VAL 3.5 10.3 - - - +
97P SER* 3.6 7.1 - - - -
159P MET* 3.2 5.7 - - - +
160P TRP* 2.8 45.2 + - + -
162P SER 2.6 20.8 + - - -
163P VAL* 3.4 3.6 - - - -
164P LEU* 2.8 31.2 + - + -
169P ILE* 3.7 29.2 - - + -
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Residues in contact with LEU 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33P PHE* 4.2 9.6 - - + -
34P THR* 1.3 76.4 - - - +
36P CYS* 1.3 63.3 + - - +
37P PHE* 4.0 13.6 - - + -
50P PHE* 3.5 49.4 - - + -
61P LEU* 5.0 4.3 - - + -
63P VAL* 4.0 20.6 - - + -
94P ILE 3.7 1.2 - - - +
95P CYS* 3.2 1.6 - - - -
96P VAL* 2.8 45.0 + - + +
157P LEU* 3.7 26.7 - - + -
158P TYR 3.4 14.1 - - - +
159P MET* 4.0 13.2 - - + -
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Residues in contact with CYS 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34P THR* 4.2 8.1 - - - -
35P LEU* 1.3 75.0 - - - +
37P PHE* 1.3 65.6 + - - +
93P HIS* 4.2 8.3 - - + +
94P ILE 3.2 4.0 - - - -
95P CYS* 2.0 46.9 - - - -
156P ASP 3.4 2.9 - - - +
157P LEU* 3.2 0.7 - - - +
158P TYR* 2.7 36.9 + - + +
160P TRP* 3.6 30.5 - - + -
164P LEU* 4.8 0.7 - - - -
169P ILE* 4.3 2.2 - - - -
172P ALA* 4.1 8.7 - - + -
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Residues in contact with PHE 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35P LEU* 4.0 30.5 - - + -
36P CYS* 1.3 79.5 - - - +
38P ARG* 1.3 70.9 + - - +
39P ALA* 4.3 1.8 - - + -
49P LEU* 3.7 48.0 - - + -
50P PHE* 4.6 5.2 - - + -
63P VAL* 4.4 7.2 - - + -
93P HIS* 3.5 9.4 + - - -
94P ILE* 2.8 67.8 + - + +
96P VAL* 5.7 0.7 - - + -
154P ILE* 4.5 9.0 - - + -
155P GLY 3.6 7.9 - - - +
156P ASP 3.3 10.8 - - - -
157P LEU* 3.8 24.0 - - + -
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Residues in contact with ARG 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P PHE* 1.3 75.0 - - - +
39P ALA* 1.3 62.2 + - - +
92P VAL 3.3 9.2 - - - +
93P HIS* 3.6 25.6 - - + +
154P ILE* 3.3 8.3 - - - +
155P GLY 2.9 35.7 + - - +
156P ASP* 2.8 33.1 + - + +
172P ALA 3.4 16.0 + - - -
173P TYR* 2.9 33.9 + - - -
174P GLN 4.5 0.2 - - - -
175P GLY* 3.8 13.7 - - - +
201P LEU* 4.9 2.0 - - - -
203P TRP* 3.6 18.4 - - + -
204P VAL* 3.6 39.7 - - - +
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Residues in contact with ALA 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P PHE* 4.3 7.8 + - + -
38P ARG* 1.3 75.8 - - - +
40P TYR* 1.3 60.5 + - - +
41P SER* 4.2 1.1 - - - -
47P TYR* 6.0 0.7 - - - +
49P LEU* 3.7 30.1 - - + -
90P ALA 4.2 0.5 - - - +
91P PRO* 3.5 1.6 - - - +
92P VAL* 2.9 48.3 + - + +
150P PHE* 4.4 6.7 - - + -
153P GLU 3.2 8.7 - - - +
154P ILE* 4.4 2.0 - - + -
203P TRP* 3.8 3.3 - - - -
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Residues in contact with TYR 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39P ALA* 1.3 74.5 - - - +
41P SER* 1.3 62.3 + - - +
89P PRO* 4.7 7.5 + - + +
90P ALA* 3.8 11.7 - - - -
91P PRO* 3.5 35.1 - - + +
150P PHE* 4.5 0.4 - - - -
152P GLY* 3.4 3.1 - - - -
153P GLU* 2.8 38.5 + - + +
203P TRP* 3.5 56.3 - + + +
83Q LYS 5.2 2.8 + - - -
112Q THR* 5.1 3.3 - - - +
113Q PRO 2.7 29.8 + - - -
114Q LEU* 3.5 13.1 - - - +
115Q VAL* 3.5 38.4 - - + +
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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