Contacts of the strand formed by residues 32 - 40 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30I LEU* 3.6 9.6 - - - +
31I GLN* 1.3 109.3 + - - +
33I PHE* 1.3 67.4 + - - +
98I TRP 3.5 7.2 - - - +
99I GLU* 3.7 23.4 - - - +
100I SER 3.8 1.0 + - - -
101I SER* 5.1 0.7 + - - -
161I ASP* 3.3 31.1 + - - +
162I SER* 3.8 11.5 - - - +
163I VAL* 4.2 8.1 - - + +
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Residues in contact with PHE 33 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I LEU* 4.2 12.3 - - + -
32I ASN* 1.3 78.7 - - - +
34I THR* 1.3 71.1 + - - +
35I LEU* 4.0 7.0 - - + -
61I LEU* 3.6 42.2 - - + -
73I LEU* 4.2 6.7 - - + -
75I ILE* 3.7 15.0 - - + -
96I VAL* 3.8 19.7 - - + -
97I SER* 3.1 5.0 - - - -
98I TRP* 3.1 67.4 + + + +
125I VAL* 4.7 3.8 - - + -
159I MET* 3.9 21.1 - - + -
160I TRP 3.2 14.8 - - - +
162I SER 3.2 10.2 + - - +
163I VAL* 4.4 0.2 - - - +
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Residues in contact with THR 34 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I PHE* 1.3 77.7 + - - +
35I LEU* 1.3 63.2 + - - +
36I CYS* 4.1 6.7 - - - -
96I VAL 3.4 10.8 - - - +
97I SER* 3.5 7.9 - - - -
159I MET* 3.2 6.2 - - - +
160I TRP* 2.8 43.8 + - + -
162I SER 2.6 23.2 + - - -
163I VAL* 3.4 1.7 - - - -
164I LEU* 2.9 27.5 + - + -
169I ILE* 3.7 30.3 - - + -
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Residues in contact with LEU 35 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I PHE* 4.0 6.9 - - + -
34I THR* 1.3 75.5 - - - +
36I CYS* 1.3 62.8 + - - +
37I PHE* 3.8 19.4 - - + -
50I PHE* 3.5 47.8 - - + -
61I LEU* 5.2 2.9 - - + -
63I VAL* 3.9 14.6 - - + -
94I ILE 3.8 1.2 - - - +
95I CYS* 3.2 1.9 - - - -
96I VAL* 2.8 47.2 + - + +
157I LEU* 3.8 26.2 - - + -
158I TYR 3.4 15.5 - - - +
159I MET* 4.0 15.3 - - + -
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Residues in contact with CYS 36 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I THR* 4.1 8.1 - - - -
35I LEU* 1.3 75.1 - - - +
37I PHE* 1.3 67.2 + - - +
93I HIS* 4.2 8.5 - - + +
94I ILE 3.1 4.3 - - - -
95I CYS* 2.0 45.1 - - - -
156I ASP 3.8 2.9 - - - +
157I LEU* 3.3 1.0 - - - +
158I TYR* 2.8 34.9 + - + +
160I TRP* 3.6 31.6 - - + -
169I ILE* 4.2 3.4 - - - -
172I ALA* 4.1 9.2 - - + -
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Residues in contact with PHE 37 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I LEU* 3.8 32.1 - - + -
36I CYS* 1.3 80.7 - - - +
38I ARG* 1.3 66.5 + - - +
39I ALA* 4.5 2.9 - - + -
49I LEU* 3.4 48.2 - - + -
50I PHE* 4.7 3.6 - - + -
63I VAL* 4.2 8.5 - - + -
93I HIS* 3.6 9.6 + - - -
94I ILE* 2.8 70.1 + - + +
96I VAL* 5.5 0.4 - - + -
154I ILE* 4.6 9.2 - - + -
155I GLY 3.7 8.7 - - - +
156I ASP 3.3 10.5 - - - -
157I LEU* 3.9 21.8 - - + -
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Residues in contact with ARG 38 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I PHE* 1.3 73.7 - - - +
39I ALA* 1.3 59.8 + - - +
92I VAL 3.3 9.9 - - - +
93I HIS* 3.7 28.0 - - + +
154I ILE* 3.3 7.4 - - - +
155I GLY* 2.9 38.9 + - - +
156I ASP* 2.6 31.6 + - + +
172I ALA 3.2 15.8 + - - -
173I TYR* 2.9 35.0 + - - -
174I GLN 4.4 0.4 - - - -
175I GLY* 3.8 13.9 - - - +
201I LEU* 4.7 2.4 - - - +
203I TRP* 3.8 17.9 - - + -
204I VAL* 3.5 38.2 - - - +
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Residues in contact with ALA 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I PHE* 4.3 8.6 + - + -
38I ARG* 1.3 75.3 - - - +
40I TYR* 1.3 61.4 + - - +
41I SER* 4.2 0.9 - - - +
47I TYR* 5.9 1.1 - - - +
49I LEU* 4.1 25.1 - - + -
90I ALA 4.2 0.5 - - - +
91I PRO* 3.6 1.0 - - - +
92I VAL* 2.9 47.7 + - + +
94I ILE* 4.9 1.1 - - + -
150I PHE* 4.2 9.2 - - + -
153I GLU 3.2 8.7 - - - +
154I ILE* 4.3 4.7 - - + -
203I TRP* 3.9 3.5 - - - -
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Residues in contact with TYR 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I ALA* 1.3 75.5 - - - +
41I SER* 1.3 61.9 + - - +
89I PRO* 4.7 7.1 + - + +
90I ALA* 3.8 12.6 - - - -
91I PRO* 3.6 33.7 - - + +
152I GLY* 3.4 3.6 - - - -
153I GLU* 2.9 37.9 + - + +
203I TRP* 3.5 55.4 - + + +
83J LYS 5.2 2.6 + - - -
112J THR* 5.0 3.8 - - - +
113J PRO 2.7 30.0 + - - -
114J LEU* 3.4 14.1 - - - +
115J VAL* 3.6 37.9 + - + +
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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