Contacts of the strand formed by residues 46 - 58 (chain B) in PDB entry 5GKI
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 46 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A ALA 4.1 0.2 - - - +
128A LEU* 3.4 2.7 - - - +
129A THR* 2.8 50.7 + - + +
239A LYS* 4.1 19.7 + - + +
240A ARG 3.2 26.1 + - - -
41B TYR* 3.4 13.7 - - - +
42B ASP* 3.2 28.3 - - + +
45B ALA* 1.3 77.3 - - - +
47B SER* 1.3 67.1 + - - +
48B GLU* 6.1 4.9 - - + +
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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
----------------------------------------------------------
126A LEU* 3.3 16.3 - - - +
127A ALA 3.0 13.2 - - - -
128A LEU* 4.1 12.3 - - - -
39B VAL 5.4 0.5 + - - -
40B HIS* 3.9 0.2 - - - -
41B TYR* 2.9 45.6 + - - +
46B LYS* 1.3 77.2 - - - +
48B GLU* 1.3 70.1 + - - +
76B ASN* 3.2 26.4 + - - -
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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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125A GLU 4.5 0.9 - - - +
126A LEU* 3.6 3.8 - - - +
127A ALA* 2.8 44.2 + - + +
39B VAL 3.7 3.1 - - - +
40B HIS* 2.6 52.5 + - - +
46B LYS* 6.1 5.3 - - + +
47B SER* 1.3 80.6 - - - +
49B LEU* 1.3 61.6 + - - +
50B GLY 4.2 0.8 + - - -
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Residues in contact with LEU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLU 3.9 12.1 - - - +
125A GLU 3.5 9.6 - - - +
126A LEU* 3.4 37.9 - - + +
38B LYS* 3.3 5.0 - - - +
39B VAL* 3.0 51.6 + - + +
48B GLU* 1.3 76.3 + - - +
50B GLY* 1.3 66.7 + - - +
54B ARG* 3.5 33.0 - - - +
68B GLN* 4.1 4.7 - - - +
75B VAL* 3.6 35.2 - - + -
76B ASN* 4.3 0.9 - - - +
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Residues in contact with GLY 50 (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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124A GLU* 3.8 21.4 + - - +
125A GLU 5.2 1.0 + - - -
37B CYS 3.9 0.9 - - - -
38B LYS* 4.1 7.6 - - - -
48B GLU 4.2 0.6 + - - -
49B LEU* 1.3 76.3 - - - +
51B SER* 1.3 56.0 + - - -
54B ARG* 2.6 38.7 + - - -
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Residues in contact with SER 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ASP* 4.3 0.7 - - - +
123A TYR 5.1 2.1 + - - -
124A GLU* 3.4 19.3 + - - +
36B ARG* 3.1 17.9 - - - -
37B CYS 3.1 8.7 - - - -
38B LYS* 3.7 11.4 - - - +
50B GLY* 1.3 71.5 - - - +
52B GLY* 1.3 55.8 + - - +
54B ARG* 3.8 0.2 - - - -
110B GLU* 2.2 32.7 + - - -
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Residues in contact with GLY 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU 3.9 5.4 - - - -
122A ASP* 3.8 7.4 - - - -
35B ALA 3.5 0.3 - - - +
36B ARG* 4.0 5.6 - - - -
37B CYS 2.9 27.9 + - - +
50B GLY 3.4 1.8 + - - -
51B SER* 1.3 76.3 + - - +
53B ASP* 1.3 67.7 + - - -
54B ARG* 3.3 22.6 - - - -
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Residues in contact with ASP 53 (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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5A LYS* 3.0 22.5 + - - -
30A MET* 4.6 2.1 - - - +
118A PHE* 3.5 18.8 - - + -
120A ALA* 3.6 10.8 - - + +
121A GLU* 2.6 44.4 + - - +
122A ASP* 3.8 12.9 - - - +
35B ALA 3.3 5.6 - - - +
36B ARG* 3.5 13.2 + - - +
52B GLY* 1.3 71.4 - - - -
54B ARG* 1.3 65.7 + - - +
68B GLN* 5.0 1.6 - - - -
69B SER 5.2 0.5 + - - -
113B TYR* 2.8 33.3 + - - -
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Residues in contact with ARG 54 (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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30A MET* 4.5 1.1 - - - -
118A PHE* 3.4 12.0 - - - -
122A ASP* 2.7 40.9 + - - +
124A GLU* 3.5 12.7 + - - +
33B ILE 3.9 0.3 - - - +
34B PHE* 3.7 0.5 - - - -
35B ALA 3.0 29.8 + - - +
37B CYS* 2.9 34.8 + - - -
38B LYS* 4.5 0.8 - - - +
39B VAL* 4.6 1.2 - - - +
49B LEU* 3.5 31.5 + - - +
50B GLY 2.6 30.5 + - - -
52B GLY 3.3 20.6 + - - +
53B ASP* 1.3 74.8 - - - +
55B VAL* 1.3 61.0 + - - +
56B ILE* 4.8 2.4 - - + +
66B ILE* 4.0 20.4 - - + -
67B HIS 3.4 14.6 - - - +
68B GLN* 3.9 11.7 - - + -
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Residues in contact with VAL 55 (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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30A MET* 3.7 30.7 - - + -
32A THR* 4.9 4.5 - - + +
57A ILE* 4.2 20.0 - - + -
118A PHE* 3.8 16.8 - - + -
32B THR* 4.3 2.7 - - + -
33B ILE 3.5 3.4 - - - +
34B PHE* 3.9 23.3 - - + -
54B ARG* 1.3 73.6 - - - +
56B ILE* 1.3 71.5 + - - +
57B ILE* 4.2 18.8 - - + -
65B LEU 3.8 0.4 - - - +
66B ILE* 3.4 2.3 - - - +
67B HIS* 2.8 42.6 + - + +
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Residues in contact with ILE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.7 1.4 - - + +
32B THR* 3.4 5.2 - - - +
33B ILE* 2.9 52.7 + - + +
35B ALA* 4.8 4.0 - - + -
37B CYS* 4.2 12.1 - - - -
54B ARG 4.8 3.6 - - - +
55B VAL* 1.3 80.5 - - - +
57B ILE* 1.3 69.5 + - - +
58B VAL* 4.3 2.0 - - + -
64B PHE* 3.9 30.1 - - + -
65B LEU 3.3 2.9 - - - +
66B ILE* 4.3 15.0 - - + -
94B LEU* 4.3 13.9 - - + -
107B VAL* 3.7 27.6 - - + -
109B LEU* 4.0 15.0 - - + -
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Residues in contact with ILE 57 (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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55A VAL* 4.3 17.5 - - + -
57A ILE* 3.9 27.4 - - + -
67A HIS* 5.1 7.9 - - + -
30B MET* 4.2 21.5 - - + -
31B LEU 3.3 7.4 - - - +
32B THR* 4.0 17.5 - - + +
55B VAL* 4.2 6.1 - - + -
56B ILE* 1.3 80.6 - - - +
58B VAL* 1.3 73.9 + - - +
59B LYS* 4.4 8.7 - - + -
63B SER 3.9 0.3 - - - +
64B PHE* 3.3 4.2 - - - -
65B LEU* 2.7 58.9 + - + +
67B HIS* 5.2 4.7 - - + -
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Residues in contact with VAL 58 (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 LEU* 4.3 17.3 - - + -
29B ALA 3.7 2.3 - - - +
30B MET* 3.6 3.3 - - - -
31B LEU* 3.0 56.3 + - + +
56B ILE* 4.7 2.2 - - + -
57B ILE* 1.3 79.5 - - - +
59B LYS* 1.3 71.0 + - - +
62B GLY* 5.1 1.3 - - - +
63B SER 3.5 7.2 - - - +
64B PHE* 3.8 28.9 - - + -
84B VAL* 4.0 26.2 - - + -
94B LEU* 4.4 5.4 - - + -
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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