Contacts of the strand formed by residues 32 - 40 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30L LEU* 4.0 9.6 - - - +
31L GLN* 1.3 111.1 + - + +
33L PHE* 1.3 67.0 - - - +
98L TRP 3.4 6.5 - - - +
99L GLU* 3.4 25.9 + - - +
100L SER* 3.8 1.7 + - - -
101L SER* 5.1 1.2 + - - -
161L ASP* 2.9 31.0 + - - +
162L SER* 3.9 11.8 - - - +
163L VAL* 4.1 11.0 - - + +
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Residues in contact with PHE 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L LEU* 4.3 8.7 - - + -
32L ASN* 1.3 76.2 - - - +
34L THR* 1.3 70.9 + - - +
35L LEU* 4.0 9.4 - - + -
61L LEU* 3.5 38.8 - - + -
73L LEU* 4.3 7.4 - - + -
75L ILE* 3.6 17.7 - - + -
96L VAL* 3.8 20.2 - - + -
97L SER* 3.2 4.0 - - - -
98L TRP* 2.9 69.7 + + + +
125L VAL* 4.6 7.6 - - + -
159L MET* 3.9 20.9 - - + -
160L TRP 3.2 13.9 - - - +
161L ASP* 4.6 0.4 - - - -
162L SER 3.2 9.5 - - - +
163L VAL* 4.4 0.3 - - - +
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Residues in contact with THR 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PHE* 1.3 76.6 + - - +
35L LEU* 1.3 63.6 + - - +
36L CYS* 4.3 6.1 - - - -
95L CYS* 4.9 0.2 - - + -
96L VAL 3.4 11.9 - - - +
97L SER* 3.5 8.6 - - - -
159L MET* 3.3 5.2 - - - +
160L TRP* 2.9 43.4 + - + +
162L SER 2.7 20.4 + - - -
163L VAL* 3.3 2.3 - - - -
164L LEU* 2.9 26.5 + - + -
169L ILE* 3.7 30.1 - - + -
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Residues in contact with LEU 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PHE* 4.0 11.6 - - + -
34L THR* 1.3 74.3 - - - +
36L CYS* 1.3 65.5 + - - +
37L PHE* 3.8 23.4 - - + -
50L PHE* 3.6 56.5 - - + -
61L LEU* 5.5 1.1 - - + -
63L VAL* 3.9 16.2 - - + -
94L ILE 3.8 0.9 - - - +
95L CYS* 3.2 1.9 - - - -
96L VAL* 2.8 44.7 + - + +
157L LEU* 3.9 14.6 - - + -
158L TYR 3.5 15.0 - - - +
159L MET* 4.0 11.2 - - + -
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Residues in contact with CYS 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34L THR* 4.3 1.1 - - - -
35L LEU* 1.3 75.3 - - - +
37L PHE* 1.3 65.9 + - - +
93L HIS* 4.1 9.0 - - - +
94L ILE 3.2 4.0 - - - +
95L CYS* 2.0 46.2 - - - -
156L ASP 3.9 3.1 - - - +
157L LEU* 3.3 0.5 - - - -
158L TYR* 2.8 35.1 + - + +
160L TRP* 3.6 29.3 - - + -
164L LEU* 4.8 0.2 - - - -
169L ILE* 4.1 9.0 - - - -
172L ALA* 4.1 11.0 - - + -
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Residues in contact with PHE 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L LEU* 3.8 33.7 - - + -
36L CYS* 1.3 80.4 - - - +
38L ARG* 1.3 68.2 + - - +
39L ALA* 4.4 2.9 - - + -
49L LEU* 3.4 48.7 - - + -
50L PHE* 4.6 4.5 - - + -
63L VAL* 4.2 11.7 - - + -
92L VAL 4.1 0.2 - - - +
93L HIS* 3.6 8.3 + - - -
94L ILE* 2.8 66.5 + - + +
96L VAL* 5.7 0.7 - - + -
154L ILE* 4.7 9.6 - - + -
155L GLY 3.8 7.2 - - - +
156L ASP 3.4 10.1 - - - -
157L LEU* 3.9 21.3 - - + -
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Residues in contact with ARG 38 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 1.3 73.8 - - - +
39L ALA* 1.3 60.4 + - - +
92L VAL 3.3 11.4 - - - +
93L HIS* 3.7 24.8 - - + +
153L GLU 3.9 0.2 - - - +
154L ILE* 3.3 6.1 - - - +
155L GLY* 2.8 42.2 + - - +
156L ASP* 2.8 31.4 + - + +
172L ALA 3.3 24.4 + - - -
173L TYR* 3.3 23.6 + - - -
175L GLY* 4.1 10.9 - - - -
201L LEU* 4.6 2.7 - - - -
203L TRP* 3.7 20.3 - - + -
204L VAL* 3.3 40.2 - - - +
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Residues in contact with ALA 39 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L PHE* 4.2 8.9 + - + -
38L ARG* 1.3 74.6 - - - +
40L TYR* 1.3 61.5 + - - +
41L SER 5.5 0.2 - - - +
47L TYR* 6.0 0.9 - - - +
49L LEU* 4.0 27.1 - - + -
90L ALA 4.4 0.3 - - - +
91L PRO* 3.6 0.9 - - - +
92L VAL* 2.9 48.2 + - + +
94L ILE* 4.8 0.9 - - + +
150L PHE* 4.3 4.7 - - + -
153L GLU 3.3 8.7 - - - +
154L ILE* 4.2 7.2 - - + -
203L TRP* 3.9 3.8 - - - -
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Residues in contact with TYR 40 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ALA* 1.3 75.3 - - - +
41L SER* 1.3 64.4 + - - +
89L PRO* 4.8 7.8 + - + +
90L ALA* 3.9 11.2 - - - -
91L PRO* 3.6 35.0 - - + +
150L PHE* 4.5 0.2 - - - -
152L GLY* 3.4 3.5 - - - -
153L GLU* 2.8 37.8 + - + +
203L TRP* 3.5 55.2 - + + +
83M LYS 5.2 2.4 + - - -
112M THR* 5.2 2.4 - - - +
113M PRO 2.8 29.0 + - - -
114M LEU* 3.6 13.0 - - - +
115M VAL* 3.5 37.3 + - + +
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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