Contacts of the strand formed by residues 37 - 48 (chain B) in PDB entry 3HKS
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 ARG 37 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B ILE 3.5 0.7 - - - +
33B VAL* 3.3 4.5 - - - +
34B ILE 2.9 31.1 + - - +
35B LYS* 3.4 15.5 - - + +
36B ASN* 1.3 86.4 + - - +
38B PRO* 1.4 74.6 - - - +
39B CYS* 3.5 3.1 + - - -
63B ASP* 2.8 42.4 + - - +
65B PHE* 3.9 16.4 - - - +
66B THR* 4.3 7.0 + - - -
70B LEU* 4.0 16.6 - - + -
144B MET* 4.2 3.1 - - - -
146B GLU* 3.7 24.9 + - - -
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Residues in contact with PRO 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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31B HIS* 5.4 0.2 - - - -
32B ILE 3.9 3.6 - - - +
33B VAL* 4.9 0.2 - - - -
36B ASN 4.2 2.0 - - - +
37B ARG* 1.4 99.1 - - + +
39B CYS* 1.3 58.3 + - - +
63B ASP* 3.6 4.6 - - - +
64B ILE* 3.0 31.7 + - + +
65B PHE* 3.8 27.6 - - + -
83B PRO* 3.8 15.7 - - + -
85B VAL* 5.1 0.4 - - + -
143B SER* 3.4 25.4 - - - +
144B MET* 3.8 18.5 - - + -
146B GLU* 5.8 0.2 - - - +
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Residues in contact with CYS 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B HIS* 3.2 12.1 + - - -
32B ILE* 3.0 37.7 + - + +
34B ILE* 4.4 10.5 - - - -
37B ARG* 3.6 15.9 - - - -
38B PRO* 1.3 76.4 - - - +
40B LYS* 1.3 60.6 + - - +
41B VAL 3.8 0.2 + - - -
61B ALA* 3.4 23.6 - - + -
62B ILE 3.2 8.7 - - - +
63B ASP* 3.9 11.0 - - - -
64B ILE* 4.0 0.9 - - - -
70B LEU* 3.7 31.4 - - - -
83B PRO* 4.6 1.0 - - - +
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Residues in contact with LYS 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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29B GLY* 2.8 38.3 + - - +
30B GLY 3.6 5.6 - - - +
31B HIS* 3.6 27.2 + - + -
39B CYS* 1.3 71.5 - - - +
41B VAL* 1.3 66.2 - - - +
42B VAL* 3.5 11.3 + - + +
61B ALA* 3.2 2.3 - - - -
62B ILE* 2.7 44.2 + - + +
64B ILE* 3.7 6.5 - - + +
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Residues in contact with VAL 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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26B ILE* 3.8 20.4 - - + -
27B ARG 3.7 12.3 - - - +
28B LYS* 3.8 4.1 - - - +
29B GLY* 2.7 29.5 + - - -
30B GLY 2.8 24.3 + - - +
32B ILE* 3.7 29.6 - - + -
40B LYS* 1.3 72.2 - - - +
42B VAL* 1.3 63.5 + - - +
43B GLU 3.8 10.3 - - - +
44B VAL* 3.6 30.5 - - + -
59B PHE* 4.6 6.5 - - + -
60B VAL 3.8 5.6 - - - +
61B ALA* 4.1 2.5 - - + -
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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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28B LYS* 3.5 31.5 - - - +
40B LYS* 3.5 12.1 + - + +
41B VAL* 1.3 77.2 - - - +
43B GLU* 1.3 62.8 + - + +
60B VAL* 2.9 36.8 + - + +
62B ILE* 3.7 35.4 - - + -
69B LYS* 5.2 2.7 - - - +
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Residues in contact with GLU 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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28B LYS* 4.9 3.1 - - - -
41B VAL* 3.7 2.1 - - - +
42B VAL* 1.3 84.5 - - + +
44B VAL* 1.3 77.4 + - - +
45B SER* 4.9 6.6 - - - +
58B HIS 4.3 0.4 - - - +
59B PHE* 3.5 4.3 - - - -
60B VAL* 2.9 53.8 + - + +
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Residues in contact with VAL 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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26B ILE 4.0 15.9 - - - +
27B ARG* 4.1 4.0 - - - +
28B LYS* 3.8 18.1 - - + +
41B VAL* 3.6 21.8 - - + -
43B GLU* 1.3 84.1 - - - +
45B SER* 1.3 62.6 + - - +
46B THR* 3.6 20.6 + - - +
57B CYS* 4.4 3.4 - - + -
58B HIS 3.4 3.6 - - - +
59B PHE* 3.9 26.7 - - + -
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Residues in contact with SER 45 (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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43B GLU* 4.3 8.0 - - - -
44B VAL* 1.3 73.8 - - - +
46B THR* 1.3 60.4 + - - +
47B SER* 4.2 7.7 + - - -
56B LYS 3.7 1.4 - - - +
57B CYS* 3.5 0.5 - - - -
58B HIS* 2.7 56.2 + - - +
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Residues in contact with THR 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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24B GLY* 6.3 0.2 - - - -
44B VAL* 3.6 18.4 - - - +
45B SER* 1.3 73.6 + - - +
47B SER* 1.3 66.6 + - - +
48B LYS* 3.9 21.4 + - - +
55B ALA* 4.1 17.9 - - + -
56B LYS 3.3 9.9 - - - +
57B CYS* 3.7 20.7 - - - -
76B SER* 5.3 0.9 - - - -
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Residues in contact with SER 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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45B SER* 4.2 7.5 + - - -
46B THR* 1.3 78.9 + - - +
48B LYS* 1.3 67.6 + - - +
49B THR* 3.6 10.6 - - - +
55B ALA* 4.0 1.6 - - - -
56B LYS* 2.7 39.6 + - - +
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Residues in contact with LYS 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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46B THR* 3.9 29.7 + - - +
47B SER* 1.3 74.6 - - - +
49B THR* 1.3 59.0 + - - +
50B GLY 4.5 1.4 + - - +
53B GLY* 3.4 21.8 - - - -
54B HIS 3.9 4.7 - - - +
55B ALA* 3.9 12.6 - - + +
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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