Contacts of the strand formed by residues 40 - 49 (chain B) in PDB entry 4HXG
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 LYS 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35B ASN* 3.0 31.8 + - - +
38B SER* 3.1 30.3 + - - +
39B ASN* 1.3 81.3 - - - +
41B TYR* 1.3 67.6 + - - +
42B GLU* 4.9 3.4 - - + -
586B PRO* 3.8 5.4 - - - +
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Residues in contact with TYR 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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16B TYR* 6.3 2.5 - + - -
32B THR* 4.2 18.4 - - + -
33B LYS 3.6 13.0 - - - +
34B ALA* 3.7 23.3 - - + -
40B LYS* 1.3 78.0 - - - +
42B GLU* 1.3 62.3 + - - +
43B ASN* 4.0 12.6 + - - +
582B ILE 3.7 5.6 + - - -
583B ARG* 4.1 8.5 - - - -
584B GLY 2.6 30.7 + - - -
585B SER* 4.3 1.7 - - - -
586B PRO* 4.2 14.3 - - + +
589B ARG* 3.2 28.5 + - - -
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Residues in contact with GLU 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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31B LEU 3.6 1.4 - - - +
32B THR* 3.2 7.1 - - - +
33B LYS* 3.0 47.4 + - + +
35B ASN* 2.9 42.3 + - + +
38B SER* 4.5 1.9 + - - +
40B LYS* 4.5 3.4 - - + +
41B TYR* 1.3 75.7 - - - +
43B ASN* 1.3 61.5 + - - +
44B THR* 4.3 4.3 - - - +
60B ASP* 5.3 7.6 - - - +
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Residues in contact with ASN 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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30B VAL* 4.2 9.0 - - + +
31B LEU 3.6 1.8 - - - -
32B THR* 2.5 36.4 + - - +
41B TYR* 4.0 12.5 + - - +
42B GLU* 1.3 73.7 - - - +
44B THR* 1.3 64.5 + - - +
59B GLU* 3.6 0.7 - - - +
60B ASP* 2.9 34.1 + - - +
61B ALA 3.2 22.7 + - - +
62B SER* 4.6 11.0 + - - -
78B PHE* 6.3 0.6 - - - -
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Residues in contact with THR 44 (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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30B VAL* 4.5 2.0 - - - +
31B LEU* 2.7 58.4 + - + +
42B GLU* 5.0 3.5 - - - +
43B ASN* 1.3 75.7 + - - +
45B ILE* 1.3 72.9 + - - +
46B VAL* 4.7 2.5 - - + -
57B PHE* 4.2 24.0 - - + -
58B ILE 3.8 6.5 - - - +
59B GLU* 2.6 29.6 + - - +
61B ALA 4.4 0.7 - - - -
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ALA* 4.8 1.3 - - + -
29B TYR 3.4 11.9 - - - +
30B VAL* 5.0 2.2 - - + -
44B THR* 1.3 71.2 - - - +
46B VAL* 1.3 64.0 + - - +
47B ILE* 4.2 23.6 - - + -
57B PHE* 3.3 9.2 - - - +
58B ILE* 2.9 48.6 + - + +
61B ALA* 3.6 24.0 - - + +
62B SER* 4.0 11.9 - - - +
64B PRO* 3.7 30.3 - - + -
73B ILE* 4.7 1.1 - - + -
75B PHE* 3.7 32.3 - - + -
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Residues in contact with VAL 46 (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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28B ALA* 3.3 4.3 - - - -
29B TYR* 3.0 65.9 + - + +
31B LEU* 4.1 25.6 - - + -
44B THR* 3.5 2.2 + - + +
45B ILE* 1.3 78.3 - - - +
47B ILE* 1.3 65.1 + - - +
48B GLU* 3.9 2.2 - - + -
55B ARG* 3.8 31.6 - - + -
56B LYS 3.6 3.4 - - - +
57B PHE* 4.0 18.6 - - + -
338B TYR* 3.9 13.0 - - - +
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Residues in contact with ILE 47 (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 LEU* 4.4 21.1 - - + -
27B VAL 3.3 10.3 - - - +
28B ALA* 4.1 13.7 - - + -
45B ILE* 4.2 6.3 - - + -
46B VAL* 1.3 79.4 - - - +
48B GLU* 1.3 63.8 + - - +
49B ASN 4.2 0.2 + - - -
54B SER 3.7 0.3 - - - +
55B ARG* 3.3 2.4 - - - -
56B LYS* 2.8 53.9 + - + +
58B ILE* 4.0 9.9 - - + -
66B ILE* 5.8 0.7 - - + -
73B ILE* 3.7 24.5 - - + -
92B LEU* 3.9 26.2 - - + -
95B LEU* 3.9 21.8 - - + -
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Residues in contact with GLU 48 (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 LEU* 3.6 7.6 - - - +
27B VAL* 2.8 43.1 + - + +
29B TYR* 2.7 23.8 + - + -
46B VAL* 3.9 7.2 - - + -
47B ILE* 1.3 74.1 - - - +
49B ASN* 1.3 63.0 + - - +
50B LEU* 3.7 8.2 + - + +
53B GLY* 4.6 14.0 - - - +
54B SER 3.1 6.3 - - - +
55B ARG* 2.6 50.8 + - + -
325B LEU* 5.6 2.5 - - - -
335B LEU* 4.8 10.0 - - + +
336B THR* 3.6 12.3 - - - +
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Residues in contact with ASN 49 (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 ASN* 3.6 20.9 - - - +
26B LEU* 4.2 14.5 - - + +
47B ILE 4.2 0.6 + - - -
48B GLU* 1.3 70.5 - - - +
50B LEU* 1.3 70.7 + - - +
51B GLU 3.5 1.6 + - - -
52B ASP* 2.5 52.5 + - - +
53B GLY* 3.5 7.8 + - - -
54B SER* 3.0 16.2 + - - +
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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