Contacts of the strand formed by residues 35 - 40 (chain A) in PDB entry 3QPV
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 THR 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A SER 4.0 5.2 + - - -
34A PRO* 1.3 76.8 + - - +
36A VAL* 1.3 80.3 + - - +
37A ILE* 4.2 12.3 - - + +
113A LEU* 3.8 3.4 - - - +
119A GLN* 2.9 10.8 + - - -
120A ILE* 3.3 22.3 - - + +
121A ALA 2.8 26.7 + - - +
146A LYS* 3.6 24.4 - - + +
148A PHE* 4.3 14.8 - - + -
228A ASP* 4.6 1.4 + - - -
230A ILE* 4.5 10.3 - - + +
231A GLN* 4.9 6.7 + - + +
234A ILE* 6.2 1.3 - - + -
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Residues in contact with VAL 36 (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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35A THR* 1.3 74.8 - - - +
37A ILE* 1.3 65.9 + - - +
38A VAL* 3.9 20.2 + - + +
106A LEU* 5.4 3.6 - - + -
109A VAL* 3.7 29.6 - - + -
113A LEU* 3.7 12.3 - - + -
121A ALA* 3.4 4.9 - - + +
123A PHE* 4.2 13.2 - - + -
136A ILE* 4.5 10.8 - - + -
139A PHE* 4.4 7.6 - - + -
140A ALA* 5.2 3.1 - - + -
145A PHE* 3.8 19.1 - - + -
146A LYS 2.9 10.7 + - - +
147A ALA* 3.4 7.5 - - + +
148A PHE 3.0 24.1 + - - +
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Residues in contact with ILE 37 (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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35A THR* 4.2 9.2 - - + -
36A VAL* 1.3 74.3 - - - +
38A VAL* 1.3 60.3 + - - +
39A MET* 3.9 12.7 + - - -
54A LEU* 4.2 17.3 - - + -
58A LEU* 5.1 0.9 - - + -
120A ILE* 3.6 25.4 - - + -
121A ALA 2.7 12.1 + - - +
122A VAL* 3.5 12.4 - - + +
123A PHE* 2.6 36.2 + - - +
148A PHE* 3.4 18.4 - - + +
150A ILE* 3.6 26.9 - - + -
234A ILE* 3.6 30.1 - - + -
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Residues in contact with VAL 38 (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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36A VAL* 3.9 16.8 - - + +
37A ILE* 1.3 77.9 - - - +
39A MET* 1.3 72.3 + - - +
40A VAL* 3.7 3.0 + - + +
123A PHE* 3.8 4.3 - - + +
127A ASN* 4.0 17.5 - - + +
133A ARG* 5.0 0.2 - - + -
136A ILE* 3.7 38.1 - - + -
147A ALA* 5.2 2.2 - - + -
148A PHE 2.9 10.0 + - - +
149A PHE* 3.4 41.4 - - + -
150A ILE 2.9 25.9 + - - +
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Residues in contact with MET 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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37A ILE* 4.2 7.4 - - - -
38A VAL* 1.3 73.2 - - - +
40A VAL* 1.3 59.8 + - - +
47A LYS* 4.0 25.4 - - + +
50A ILE* 3.8 22.9 - - + -
51A SER* 3.4 23.6 - - - +
54A LEU* 5.8 0.4 - - - -
122A VAL* 3.9 17.9 - - + -
123A PHE 3.0 18.2 + - - +
124A ASP* 3.8 11.2 - - - +
125A ALA 3.1 14.4 - - - +
127A ASN* 3.0 28.8 + - - +
150A ILE* 3.3 44.2 - - + +
152A SER* 5.9 1.1 - - - +
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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 VAL* 3.9 11.2 - - + +
39A MET* 1.3 83.4 - - - +
41A GLY* 1.3 61.9 - - - +
47A LYS* 3.3 11.1 - - - +
126A THR 3.4 2.7 - - - +
127A ASN 3.7 22.2 - - - +
133A ARG* 3.8 26.7 - - - +
149A PHE* 4.1 10.3 - - + -
150A ILE 2.7 10.4 + - - +
151A GLU* 3.2 32.9 - - + +
152A SER 3.0 26.0 + - - -
197A TYR* 4.5 4.9 - - + -
200A LEU* 4.5 9.6 - - + -
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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