Contacts of the strand formed by residues 32 - 40 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30Q LEU* 3.5 17.6 - - - +
31Q GLN* 1.3 100.8 - - - +
33Q PHE* 1.3 69.2 + - - +
98Q TRP 3.4 5.6 - - - -
99Q GLU* 3.7 21.0 - - - +
100Q SER* 3.8 2.1 + - - -
101Q SER* 4.9 1.7 + - - -
161Q ASP 3.5 23.2 + - - +
162Q SER* 4.0 5.7 - - - +
163Q VAL* 3.9 19.1 - - + -
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Residues in contact with PHE 33 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Q LEU* 4.4 11.4 - - + -
32Q ASN* 1.3 79.7 - - - +
34Q THR* 1.3 68.9 + - - +
35Q LEU* 4.1 9.2 - - + -
61Q LEU* 3.3 37.9 - - + -
73Q LEU* 4.3 6.5 - - + -
75Q ILE* 3.6 24.7 - - + -
96Q VAL* 4.0 19.3 - - + -
97Q SER* 3.1 4.2 - - - -
98Q TRP* 3.0 59.3 + + + +
125Q VAL* 4.9 3.6 - - + -
159Q MET* 3.8 23.8 - - + -
160Q TRP 3.1 15.0 - - - +
162Q SER 3.3 9.4 + - - +
163Q VAL* 4.5 0.3 - - - -
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Residues in contact with THR 34 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q PHE* 1.3 76.5 + - - +
35Q LEU* 1.3 63.4 + - - +
36Q CYS* 4.2 7.0 - - - -
95Q CYS* 4.9 0.2 - - + -
96Q VAL 3.3 10.3 - - - +
97Q SER* 3.4 8.9 - - - -
159Q MET* 3.2 5.9 - - - +
160Q TRP* 2.8 45.5 + - + -
162Q SER 2.6 22.1 + - - -
164Q LEU* 2.9 43.8 + - + -
169Q ILE* 3.9 14.4 - - + -
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Residues in contact with LEU 35 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q PHE* 4.1 9.1 - - + -
34Q THR* 1.3 74.5 - - - +
36Q CYS* 1.3 61.4 + - - +
37Q PHE* 3.6 24.6 - - + -
50Q PHE* 3.5 45.8 - - + -
61Q LEU* 5.9 0.4 - - + -
63Q VAL* 3.9 14.1 - - + -
94Q ILE 3.8 0.9 - - - +
95Q CYS* 3.1 2.3 - - - -
96Q VAL* 2.7 49.3 + - + +
157Q LEU* 3.6 24.7 - - + -
158Q TYR 3.4 15.0 - - - +
159Q MET* 3.9 15.9 - - + -
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Residues in contact with CYS 36 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34Q THR* 4.2 7.4 - - - -
35Q LEU* 1.3 73.4 - - - +
37Q PHE* 1.3 68.2 + - - +
93Q HIS* 4.1 7.9 - - - +
94Q ILE 3.1 4.9 - - - -
95Q CYS* 2.0 46.4 - - - -
156Q ASP 3.8 2.7 - - - +
157Q LEU* 3.3 1.2 - - - +
158Q TYR* 2.8 36.6 + - + +
160Q TRP* 3.7 30.3 - - + -
164Q LEU* 4.6 0.7 - - - -
169Q ILE* 4.4 2.5 - - - -
172Q ALA* 4.2 10.1 - - + -
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Residues in contact with PHE 37 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q LEU* 3.6 32.8 - - + -
36Q CYS* 1.3 80.2 - - - +
38Q ARG* 1.3 67.1 + - - +
39Q ALA* 4.5 2.5 - - + -
49Q LEU* 3.5 46.4 - - + -
50Q PHE* 4.8 3.1 - - + -
63Q VAL* 4.3 8.1 - - + -
92Q VAL 4.1 0.3 - - - +
93Q HIS* 3.6 8.7 + - - -
94Q ILE* 2.8 68.9 + - + +
96Q VAL* 5.5 1.1 - - + -
154Q ILE* 4.4 11.0 - - + -
155Q GLY 3.8 7.0 - - - +
156Q ASP 3.3 9.8 + - - -
157Q LEU* 3.8 24.9 - - + -
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Residues in contact with ARG 38 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q PHE* 1.3 73.2 - - - +
39Q ALA* 1.3 60.7 + - - +
92Q VAL 3.3 12.6 - - - +
93Q HIS* 3.8 26.5 + - + +
153Q GLU 3.9 0.2 - - - +
154Q ILE* 3.2 7.8 - - - +
155Q GLY* 2.8 40.8 + - - +
156Q ASP* 2.6 32.9 + - + +
172Q ALA 3.2 16.6 + - - -
173Q TYR* 3.1 33.7 + - - -
174Q GLN 4.7 0.4 - - - -
175Q GLY* 4.0 11.5 - - - +
201Q LEU* 4.7 4.5 - - + +
203Q TRP* 3.7 17.5 - - + -
204Q VAL* 3.6 36.6 - - - +
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Residues in contact with ALA 39 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Q PHE* 4.2 8.9 + - + -
38Q ARG* 1.3 76.0 - - - +
40Q TYR* 1.3 61.9 + - - +
41Q SER* 4.2 0.9 - - - -
47Q TYR* 6.0 0.9 - - - +
49Q LEU* 4.4 15.9 - - + -
90Q ALA 4.2 0.3 - - - +
91Q PRO* 3.6 0.5 - - - +
92Q VAL* 2.8 48.0 + - + +
94Q ILE* 4.7 1.6 - - + -
150Q PHE* 4.4 13.9 - - + -
153Q GLU 3.2 8.7 - - - +
154Q ILE* 4.4 6.1 - - + -
203Q TRP* 3.8 2.9 - - - -
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Residues in contact with TYR 40 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39Q ALA* 1.3 76.1 - - - +
41Q SER* 1.3 62.1 + - - +
89Q PRO* 4.7 6.9 + - + +
90Q ALA* 3.6 14.1 - - - -
91Q PRO* 3.4 36.7 - - + +
153Q GLU* 2.8 35.8 + - + -
203Q TRP* 3.6 53.6 - + + +
83R LYS 5.3 2.4 + - - -
112R THR* 4.9 4.5 - - - +
113R PRO 2.8 28.6 + - - -
114R LEU* 3.5 14.0 - - - +
115R VAL* 3.5 43.1 + - + +
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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