Contacts of the strand formed by residues 35 - 43 (chain B) in PDB entry 3HPN
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 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ARG* 3.3 35.9 - - - +
126A SER 6.1 0.2 - - - +
129A PHE* 3.7 49.1 - - + -
130A GLU* 6.6 0.2 - - - -
31B ILE* 3.3 3.0 - - - -
32B MET 2.9 32.5 + - - +
33B ASN 3.0 2.7 + - - +
34B ASP* 1.3 79.9 - - - +
36B PRO* 1.3 82.4 - - + +
37B ILE* 3.3 5.0 + - + +
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Residues in contact with PRO 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A PHE* 6.1 0.5 - - - +
132A ARG* 4.9 2.3 + - - -
29B GLN* 3.7 28.0 - - + +
30B ASN 3.5 6.7 - - - +
31B ILE* 4.6 1.6 - - + -
34B ASP 3.6 8.5 - - - +
35B MET* 1.3 98.8 - - + +
37B ILE* 1.3 59.0 + - - +
38B TYR* 3.9 19.1 + - + +
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Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET* 6.0 1.6 - - + -
129A PHE* 5.3 6.3 - - + +
132A ARG* 3.3 42.6 - - + +
134A VAL* 5.7 8.1 - - + -
28B MET 4.0 0.3 - - - +
29B GLN* 4.6 0.2 - - - -
30B ASN* 2.6 55.6 + - + +
31B ILE 4.2 0.2 - - - +
32B MET* 4.1 17.7 - - + +
35B MET* 3.6 13.2 - - + +
36B PRO* 1.3 70.4 - - - +
38B TYR* 1.3 63.0 - - - +
39B MET* 4.0 9.5 - - + +
165B LEU* 4.4 12.6 - - + -
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Residues in contact with TYR 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ARG* 3.2 23.8 + - - +
7B PHE* 3.5 22.2 - - + +
13B GLU* 3.9 36.2 + - + -
27B LEU* 3.9 15.9 - - + -
28B MET 3.2 15.5 - - - -
29B GLN* 2.8 33.7 + - + -
36B PRO* 3.9 25.5 - - + +
37B ILE* 1.3 78.4 - - - +
39B MET* 1.3 64.0 + - - +
165B LEU* 3.8 4.2 - - - +
103D TYR* 3.9 15.9 - - - -
106D ASN* 3.1 27.3 + - - -
108D GLN* 3.8 3.5 - - - +
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Residues in contact with MET 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE 4.0 9.4 - - - +
32A MET* 3.6 17.9 - - + +
33A ASN 5.8 0.2 - - - -
7B PHE* 3.8 7.9 - - - -
26B ASP 3.3 1.2 - - - +
27B LEU* 3.4 4.5 - - - +
28B MET* 2.9 48.4 + - + +
30B ASN* 2.9 37.0 - - + +
37B ILE* 4.0 15.5 - - + +
38B TYR* 1.3 75.3 - - - +
40B TYR* 1.3 61.5 + - - +
41B SER* 4.3 12.1 - - - -
163B ALA* 4.3 7.2 - - + -
164B LEU 3.3 15.5 - - - +
165B LEU* 3.3 28.7 - - + -
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.6 26.6 - + + -
13B GLU 4.1 5.4 + - - -
16B TRP* 3.6 34.3 + + + +
18B THR* 4.1 12.9 - - + +
25B TRP* 3.6 11.8 - - + -
26B ASP* 3.6 20.0 - - - -
27B LEU* 3.6 44.1 - - + +
39B MET* 1.3 71.0 - - - +
41B SER* 1.3 59.6 + - - +
54B LEU* 3.7 49.1 - - + -
164B LEU* 2.7 44.7 + - + +
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Residues in contact with SER 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN* 4.8 10.7 + - - -
34A ASP* 5.4 2.6 + - - -
24B GLY 3.9 0.7 - - - +
25B TRP* 3.5 3.4 - - - -
26B ASP* 2.9 36.0 + - - +
28B MET* 3.6 31.3 - - - +
39B MET* 4.3 9.0 - - - -
40B TYR* 1.3 77.4 - - - +
42B VAL* 1.3 67.6 + - - +
43B CYS* 5.8 0.7 - - - +
162B VAL 3.2 12.6 + - - -
163B ALA* 4.0 12.1 - - - +
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Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B GLY* 3.5 34.8 - - - +
25B TRP* 3.8 23.1 - - + +
28B MET* 5.7 0.9 - - - -
41B SER* 1.3 79.1 + - - +
43B CYS* 1.3 65.1 + - - +
44B ASN* 4.1 15.0 - - - +
52B ASN* 4.1 0.7 - - - +
157B ASP* 3.5 45.8 - - + +
160B ALA 3.2 2.7 - - - +
161B CYS* 3.3 1.0 - - - -
162B VAL* 3.0 33.5 + - + +
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Residues in contact with CYS 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ASN 5.2 0.2 - - - -
34A ASP* 3.7 34.9 - - - +
41B SER* 5.8 0.7 - - - +
42B VAL* 1.3 74.1 - - - +
44B ASN* 1.3 67.8 + - - +
45B VAL* 3.2 11.5 + - - +
81B PHE* 3.6 22.7 - - - -
160B ALA 3.6 5.4 - - - -
161B CYS* 2.1 47.8 - - - -
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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