Contacts of the strand formed by residues 26 - 32 (chain C) 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 ASP 26 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C GLY 5.1 6.1 - - - +
23C LYS 5.1 2.1 - - - +
24C GLY 4.1 5.5 - - - +
25C TRP* 1.3 78.3 - - - +
27C LEU* 1.3 76.8 + - - +
28C MET* 3.5 24.3 + - + +
40C TYR* 3.6 5.0 - - - -
41C SER 2.9 35.1 + - - +
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7C PHE* 3.8 18.6 - - + -
13C GLU* 3.6 31.2 - - + +
14C LEU* 5.6 2.7 - - + -
26C ASP* 1.3 83.7 + - - +
28C MET* 1.3 58.5 + - - +
38C TYR* 4.0 22.2 - - + -
39C MET 3.3 16.6 - - - +
40C TYR* 3.5 39.8 - - + +
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Residues in contact with MET 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ASP* 3.5 31.2 - - + +
27C LEU* 1.3 79.9 - - - +
29C GLN* 1.3 62.4 + - - +
30C ASN* 4.1 2.2 - - - +
37C ILE 4.0 0.2 - - - +
38C TYR* 3.3 9.6 - - - -
39C MET* 3.0 43.7 + - + +
41C SER* 3.6 34.3 - - - +
42C VAL* 5.8 0.4 - - - -
31D ILE* 5.5 18.2 - - - +
34D ASP* 5.4 7.6 - - - +
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Residues in contact with GLN 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C MET* 1.3 73.2 - - - +
30C ASN* 1.3 74.4 + - - +
31C ILE* 3.3 34.4 - - - +
36C PRO* 3.9 16.9 - - + +
37C ILE 3.8 2.9 - - - +
38C TYR* 2.8 41.6 + - + -
110F ARG* 3.9 12.8 + - - -
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Residues in contact with ASN 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C MET* 4.1 3.3 - - - +
29C GLN* 1.3 82.1 - - - +
31C ILE* 1.3 64.4 + - - +
32C MET* 6.3 0.2 - - + -
37C ILE* 2.7 50.7 + - + +
39C MET* 3.0 29.4 - - + +
30D ASN* 3.4 29.8 - - - +
31D ILE* 3.3 31.6 + - - +
32D MET* 3.8 9.3 - - - +
110F ARG* 4.1 3.0 + - - +
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Residues in contact with ILE 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C GLN* 3.3 35.2 - - + +
30C ASN* 1.3 79.4 - - - +
32C MET* 1.3 64.7 + - - +
34C ASP* 3.9 32.5 - - - +
35C MET 3.4 5.8 - - - +
36C PRO* 4.6 1.8 - - + -
37C ILE* 4.6 0.2 - - - -
28D MET* 5.7 16.9 - - + +
30D ASN* 3.4 23.6 + - - +
39D MET* 4.5 5.7 - - - +
110F ARG* 5.5 8.3 - - - +
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Residues in contact with MET 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASN* 6.3 0.2 - - + -
31C ILE* 1.3 74.2 - - - +
33C ASN* 1.3 82.3 + - - +
34C ASP 3.3 0.2 - - - -
35C MET* 2.9 26.4 + - - +
37C ILE* 4.1 14.6 - - + +
30D ASN* 3.7 24.5 - - - +
37D ILE* 6.3 1.1 - - + -
39D MET* 3.7 15.7 - - + +
74D THR* 3.9 11.2 - - + -
129D PHE* 3.4 9.8 - - + -
134D VAL* 4.2 22.7 - - + -
163D ALA* 3.7 28.7 - - - -
165D LEU* 4.5 9.0 - - + -
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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