Contacts of the strand formed by residues 32 - 40 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30K LEU* 3.5 13.4 - - - +
31K GLN* 1.3 97.3 + - - +
33K PHE* 1.3 65.0 + - - +
98K TRP* 3.6 4.3 - - - -
99K GLU* 3.4 28.3 - - - +
100K SER* 3.7 2.1 + - - -
101K SER* 5.0 1.6 + - - -
161K ASP 3.1 29.3 + - - +
162K SER* 3.9 11.1 - - - +
163K VAL* 3.9 13.5 - - + +
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Residues in contact with PHE 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K LEU* 4.3 10.5 - - + -
32K ASN* 1.3 78.3 - - - +
34K THR* 1.3 69.8 + - - +
35K LEU* 4.1 8.3 - - + -
61K LEU* 3.6 39.9 - - + -
73K LEU* 4.1 9.9 - - + -
75K ILE* 3.7 15.3 - - + -
96K VAL* 3.7 21.1 - - + -
97K SER* 3.2 2.4 - - - -
98K TRP* 3.1 68.6 + + + +
125K VAL* 4.8 3.1 - - + -
159K MET* 3.8 22.9 - - + -
160K TRP 3.3 14.8 - - - +
162K SER 3.2 9.5 + - - +
163K VAL* 4.4 0.3 - - - +
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Residues in contact with THR 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K PHE* 1.3 77.5 + - - +
35K LEU* 1.3 62.9 + - - +
36K CYS* 4.3 7.9 - - - -
96K VAL 3.4 11.2 - - - +
97K SER* 3.4 10.0 - - - -
159K MET* 3.2 5.2 - - - +
160K TRP* 2.8 41.4 + - + -
162K SER 2.7 24.1 + - - -
163K VAL* 3.3 2.1 - - - -
164K LEU* 2.9 42.9 + - + -
169K ILE* 4.1 11.9 - - + -
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Residues in contact with LEU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33K PHE* 4.3 6.3 - - + -
34K THR* 1.3 76.0 - - - +
36K CYS* 1.3 61.8 + - - +
37K PHE* 3.9 14.1 - - + -
50K PHE* 3.5 54.3 - - + -
61K LEU* 4.9 4.3 - - + -
63K VAL* 3.7 21.8 - - + -
94K ILE 3.8 0.9 - - - +
95K CYS* 3.2 2.4 - - - -
96K VAL* 2.8 47.2 + - + +
157K LEU* 3.7 18.2 - - + -
158K TYR 3.4 15.3 - - - +
159K MET* 4.0 15.7 - - + -
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Residues in contact with CYS 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K THR* 4.3 7.2 - - - -
35K LEU* 1.3 75.4 - - - +
37K PHE* 1.3 66.0 + - - +
93K HIS* 4.1 9.2 - - + +
94K ILE 3.1 4.3 - - - +
95K CYS* 2.0 47.1 - - - -
156K ASP 3.8 2.2 - - - +
157K LEU* 3.3 0.3 - - - +
158K TYR* 2.8 37.4 + - + +
160K TRP* 3.7 28.7 - - + -
164K LEU* 4.7 3.8 - - - -
172K ALA* 4.2 9.0 - - + -
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Residues in contact with PHE 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K LEU* 3.9 32.3 - - + -
36K CYS* 1.3 79.7 - - - +
38K ARG* 1.3 68.9 + - - +
39K ALA* 4.5 2.5 - - + -
49K LEU* 3.8 38.8 - - + -
50K PHE* 4.6 4.5 - - + -
63K VAL* 4.1 12.1 - - + -
92K VAL 4.1 0.2 - - - +
93K HIS* 3.5 9.4 + - - -
94K ILE* 2.8 73.5 + - + +
96K VAL* 5.6 0.4 - - + -
154K ILE* 4.6 9.0 - - + -
155K GLY 3.8 6.1 - - - +
156K ASP 3.3 9.9 - - - -
157K LEU* 3.7 26.0 - - + -
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Residues in contact with ARG 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K PHE* 1.3 73.6 - - - +
39K ALA* 1.3 59.9 + - - +
92K VAL 3.3 12.6 - - - +
93K HIS* 3.8 25.8 - - + +
154K ILE* 3.2 8.0 - - - +
155K GLY* 2.8 40.7 + - - +
156K ASP* 2.8 30.6 + - + +
172K ALA 3.3 17.6 + - - -
173K TYR* 3.1 33.7 + - - -
174K GLN 4.6 0.2 - - - -
175K GLY* 4.0 12.1 - - - -
201K LEU* 5.0 4.3 - - - -
203K TRP* 3.8 17.9 - - + -
204K VAL* 3.6 41.3 - - + +
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Residues in contact with ALA 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37K PHE* 4.3 7.4 + - + -
38K ARG* 1.3 74.8 - - - +
40K TYR* 1.3 62.1 + - - +
41K SER 4.3 0.4 - - - +
47K TYR* 6.0 0.9 - - - +
49K LEU* 4.0 27.8 - - + -
90K ALA 4.4 0.5 - - - +
91K PRO* 3.6 2.3 - - - +
92K VAL* 2.8 51.4 + - + +
94K ILE* 4.7 0.4 - - + +
150K PHE* 4.4 4.7 - - + -
153K GLU 3.2 9.2 - - - +
154K ILE* 4.2 5.8 - - + -
203K TRP* 3.9 3.6 - - - -
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Residues in contact with TYR 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39K ALA* 1.3 75.8 - - - +
41K SER* 1.3 62.6 + - - +
89K PRO* 4.8 8.1 + - + +
90K ALA* 3.9 11.9 - - - -
91K PRO* 3.6 35.9 - - + +
152K GLY* 3.4 3.8 - - - -
153K GLU* 2.9 38.8 + - + +
203K TRP* 3.5 53.8 - + + +
83L LYS 5.4 1.9 + - - -
112L THR* 5.1 3.6 - - - +
113L PRO 2.8 28.3 + - - -
114L LEU* 3.6 12.1 - - - +
115L VAL* 3.6 39.3 - - + +
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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