Contacts of the strand formed by residues 38 - 45 (chain A) in PDB entry 2B92
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 MET 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 3.9 19.1 - - + -
34A ILE* 3.7 31.0 - - + -
36A GLN 3.8 6.3 - - - +
37A PRO* 1.3 81.6 - - - +
39A VAL* 1.3 60.6 + - - +
40A VAL* 4.4 7.0 - - + -
82A CYS* 4.6 1.1 - - - -
91A HIS* 5.2 0.7 - - - -
92A ILE* 3.3 11.9 - - + +
94A VAL* 4.0 21.8 - - + -
279A THR* 3.8 3.2 - - - +
280A LYS* 2.9 30.1 + - - +
288A VAL* 3.1 15.0 + - + +
289A ASN 3.8 4.7 - - - +
290A GLY* 3.7 24.7 - - - +
293A LEU* 3.7 25.8 - - - -
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 1.3 74.3 - - - +
40A VAL* 1.3 62.6 + - - +
41A VAL* 4.4 4.7 - - + -
85A HIS* 4.0 22.9 - - + +
88A LYS* 4.8 3.1 - - + -
91A HIS* 4.6 7.8 - - + -
92A ILE 3.0 6.7 + - - +
93A LEU* 3.6 21.2 - - + +
94A VAL* 2.8 27.7 + - - +
124A SER* 3.7 2.2 - - - +
277A SER* 3.6 31.2 - - - +
278A LYS 3.5 31.6 - - - +
279A THR* 4.0 8.1 - - - +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A MET* 4.0 9.6 + - + -
39A VAL* 1.3 77.2 - - - +
41A VAL* 1.3 64.7 + - - +
94A VAL* 3.4 21.5 - - + +
96A LEU* 3.9 24.9 - - + -
122A LEU 3.2 28.0 - - - +
123A SER* 3.7 8.1 - - - -
124A SER* 2.9 36.4 + - - +
125A THR 2.9 9.7 + - - +
280A LYS* 4.2 15.9 - - + -
288A VAL* 5.9 0.2 - - + -
293A LEU* 4.5 13.9 - - + -
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.4 6.7 - - + -
40A VAL* 1.3 80.0 - - - +
42A ALA* 1.3 64.4 + - - +
55A MET* 3.4 14.9 - - + +
58A LEU* 4.2 12.6 - - + -
93A LEU* 4.1 19.1 - - + -
94A VAL 2.8 8.1 + - - +
95A LEU* 4.1 10.8 - - + -
96A LEU* 2.8 27.2 + - - -
125A THR* 3.4 7.2 - - + +
127A VAL* 3.7 25.4 - - + -
273A ILE* 4.0 26.9 - - + -
277A SER* 4.5 4.0 - - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL 4.2 0.2 - - - -
41A VAL* 1.3 77.0 - - - +
43A ILE* 1.3 61.3 + - - +
55A MET* 4.6 0.2 - - - -
96A LEU* 3.6 20.4 - - + +
98A THR* 5.2 1.1 - - + -
119A ALA* 4.0 24.7 - - + +
123A SER* 3.8 21.5 - - - -
125A THR 3.0 7.0 + - - +
126A PHE* 4.6 4.0 - - + -
127A VAL* 2.8 33.5 + - - +
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Residues in contact with ILE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ALA* 1.3 79.0 - - - +
44A VAL* 1.3 60.9 + - - +
51A LYS* 4.1 39.4 - - + +
54A LEU* 4.2 19.5 - - + -
55A MET* 3.4 34.8 - - + -
96A LEU 3.4 11.5 + - - +
97A ASP* 4.2 13.2 - - - +
98A THR* 2.3 31.6 + - - +
127A VAL* 3.2 22.2 - - + +
129A ASN* 4.2 13.7 - - + -
181A THR* 5.1 0.2 - - - +
269A PHE* 6.1 0.7 - - + -
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Residues in contact with VAL 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE* 1.3 81.7 - - - +
45A GLY* 1.3 59.6 + - - +
51A LYS* 3.7 8.7 - - - -
98A THR* 3.5 13.7 - - + +
99A GLU 5.5 1.8 - - - +
101A LEU* 4.2 12.3 - - + -
115A ILE* 5.8 1.3 - - + -
116A PHE* 4.0 27.8 - - + -
119A ALA* 3.7 17.7 - - + -
126A PHE* 3.5 37.9 - - + -
127A VAL 2.9 5.5 + - - -
128A TYR* 3.3 8.6 - - + -
129A ASN 2.7 29.9 + - - -
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Residues in contact with GLY 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 1.3 84.6 - - - +
46A LEU* 1.3 65.2 + - - +
51A LYS* 3.6 8.7 + - - +
98A THR* 4.9 0.2 + - - -
100A GLY* 3.4 5.5 - - - -
101A LEU* 2.8 33.6 + - - +
128A TYR* 4.6 5.4 - - - -
129A ASN 3.4 15.5 - - - -
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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