Contacts of the strand formed by residues 22 - 28 (chain B) in PDB entry 1HC9
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 LEU 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B ILE* 4.3 2.7 - - - -
3B CYS* 3.8 6.5 - - - -
16B CYS* 4.5 0.2 - - - -
20B GLU 4.1 0.2 + - - -
21B ASN* 1.3 79.6 - - - +
23B CYS* 1.3 71.3 + - - +
44B CYS* 3.5 5.5 - - - +
45B ALA* 3.1 57.5 + - + +
46B ALA 3.8 16.6 - - - +
47B THR* 4.4 2.7 - - - +
48B CYS* 4.0 16.8 - - + +
59B CYS* 4.3 20.0 - - + -
60B CYS 3.5 14.4 - - - +
61B SER* 4.7 5.4 - - - +
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Residues in contact with CYS 23 (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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1B ILE* 3.7 16.8 - - - -
2B VAL 3.7 4.5 - - - -
3B CYS* 2.0 51.8 - - + -
22B LEU* 1.3 79.9 - - - +
24B TYR* 1.3 64.2 + - - +
43B GLY 3.5 2.0 - - - -
59B CYS* 3.3 4.9 - - - -
60B CYS* 2.8 28.8 + - - +
62B THR 4.0 0.4 - - - -
65B CYS* 3.7 23.3 - - - -
66B ASN* 3.5 18.6 - - - -
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Residues in contact with TYR 24 (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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22B LEU* 4.8 0.9 - - + -
23B CYS* 1.3 76.3 - - - +
25B ARG* 1.3 69.3 + - - +
26B LYS* 4.0 16.2 - - + -
41B GLU* 2.7 46.2 + - + +
42B LEU* 3.5 2.3 + - - -
43B GLY* 3.1 49.3 + - - -
44B CYS 3.3 23.8 - - - -
45B ALA* 3.9 14.1 - - + -
49B PRO* 4.0 17.0 - - + -
57B VAL* 5.0 1.6 - - + -
58B THR 3.1 12.3 - - - +
59B CYS* 3.8 16.2 - - - -
66B ASN* 2.9 21.0 + - - -
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Residues in contact with ARG 25 (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 TYR* 1.3 75.2 - - - +
26B LYS* 1.3 61.5 + - - +
27B MET* 4.1 23.0 - - + +
40B VAL* 4.5 1.6 - - + -
41B GLU 3.4 4.5 - - - +
42B LEU* 3.4 19.1 - - + -
56B GLU 3.7 1.0 - - - +
57B VAL* 3.4 4.0 - - - +
58B THR* 2.9 57.5 + - - +
65B CYS 4.5 2.6 + - - -
66B ASN* 3.8 10.1 - - + +
67B PRO* 2.9 49.5 + - - +
69B PRO* 4.6 9.6 - - - +
1075B IOD 3.4 21.3 - - + +
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Residues in contact with LYS 26 (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 TYR* 4.0 15.1 - - + -
25B ARG* 1.3 73.2 - - - +
27B MET* 1.3 68.2 + - - +
28B TRP* 3.9 22.8 - - + -
39B VAL 3.8 0.7 - - - +
41B GLU* 2.8 53.5 + - + +
49B PRO* 3.9 23.8 - - - +
50B SER 4.9 4.1 + - - -
55B GLU* 4.0 26.4 + - + +
56B GLU 3.2 3.8 - - - +
57B VAL* 3.8 24.5 - - + -
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Residues in contact with MET 27 (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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25B ARG* 4.1 18.4 - - + +
26B LYS* 1.3 80.1 - - - +
28B TRP* 1.3 65.7 + - - +
38B LYS* 4.2 15.9 - - + +
39B VAL 3.2 13.5 - - - +
40B VAL* 4.1 11.9 - - + -
54B TYR 4.5 0.5 - - - +
55B GLU* 3.7 0.7 - - - -
56B GLU* 2.8 75.9 + - - +
69B PRO* 4.0 27.1 - - + -
1075B IOD 3.5 12.6 - - + -
5D GLU* 4.3 12.6 - - - +
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Residues in contact with TRP 28 (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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26B LYS* 3.9 26.9 - - + -
27B MET* 1.3 81.8 - - - +
29B CYS* 1.3 75.5 + - - +
30B ASP* 4.4 6.1 - - - +
38B LYS* 3.4 9.6 - - - +
39B VAL* 2.7 58.4 + - + +
41B GLU* 3.6 37.0 - - + -
54B TYR* 4.4 18.6 - + + +
55B GLU* 4.3 26.0 - - + -
2D ARG* 3.5 27.0 - - - +
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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