Contacts of the strand formed by residues 56 - 70 (chain B) in PDB entry 5CLQ
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 GLU 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LYS* 4.2 26.2 + - - -
207A THR* 4.7 4.7 - - - -
50B PHE* 3.9 7.9 - - - -
51B ASP* 2.8 39.0 + - + +
54B SER* 2.9 41.2 + - - +
55B LYS* 1.3 79.5 - - - +
57B TRP* 1.3 63.6 + - - +
58B LYS* 4.7 8.2 - - + +
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Residues in contact with TRP 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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204A ALA* 3.3 38.0 + - + -
207A THR* 2.8 37.3 + - + +
208A ALA 3.7 8.5 - - - -
209A LEU* 3.3 20.0 - - + +
210A PRO* 4.2 27.1 - - + +
48B PHE* 3.9 8.5 - - + -
49B ARG 3.4 10.1 - - - -
50B PHE* 3.2 43.5 - + + -
56B GLU* 1.3 83.9 - - - +
58B LYS* 1.3 62.9 + - - +
103B ASN* 4.2 0.2 - - - +
111B VAL* 3.7 18.8 - - + -
126B GLN 3.5 4.7 - - - -
127B LEU 3.8 5.8 - - - -
128B ALA* 3.4 38.1 - - + -
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Residues in contact with LYS 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLU* 3.0 42.2 + - + +
36A GLU* 6.0 0.2 - - - +
38A LYS* 6.0 3.4 - - - +
48B PHE* 3.3 4.8 - - - -
49B ARG* 2.6 72.7 + - + +
51B ASP* 3.4 39.6 + - + +
53B GLU* 4.7 4.0 + - - -
54B SER* 4.8 0.7 - - - +
56B GLU* 3.7 10.5 + - + +
57B TRP* 1.3 79.0 - - - +
59B GLU* 1.3 65.7 + - - +
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Residues in contact with GLU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.0 33.6 + - - +
32A THR 4.4 1.0 - - - +
33A GLY 3.9 6.8 - - - +
34A GLU* 3.3 27.8 + - - +
35A PHE* 4.8 6.3 - - + +
152A LYS 5.8 0.2 - - - +
154A ASN* 4.8 7.4 + - - -
46B LYS* 3.2 39.8 + - - +
47B LEU 3.9 6.1 - - - +
48B PHE* 4.0 12.3 - - + -
49B ARG* 5.4 0.3 - - - +
58B LYS* 1.3 76.0 - - - +
60B ARG* 1.3 64.9 + - - +
61B GLY* 4.0 10.9 - - - +
62B ILE* 4.9 6.6 - - - +
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Residues in contact with ARG 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 3.3 27.5 + - - +
33A GLY* 3.6 5.6 - - - -
47B LEU* 2.7 28.1 + - + +
49B ARG* 3.5 57.3 - - + +
58B LYS 3.5 0.4 + - - -
59B GLU* 1.3 76.5 - - - +
61B GLY* 1.3 59.9 + - - +
82B ARG* 3.1 32.3 + - - +
89B CYS* 3.6 26.9 + - + +
116B ASP* 4.4 6.3 + - - -
118B ALA* 4.1 4.0 - - - +
119B ASP* 2.3 44.1 + - - -
125B GLU* 3.6 15.8 + - - -
127B LEU* 5.2 2.4 - - + +
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Residues in contact with GLY 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 5.1 3.1 - - - -
46B LYS* 3.8 1.4 - - - +
47B LEU* 2.8 37.2 + - - +
59B GLU* 3.8 11.3 - - - +
60B ARG* 1.3 81.2 - - - +
62B ILE* 1.3 60.9 + - - +
80B MET* 4.0 2.6 - - - +
82B ARG* 4.2 15.7 - - - -
89B CYS* 4.3 5.8 - - - -
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Residues in contact with ILE 62 (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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154A ASN* 3.7 17.0 - - - +
44B ARG* 3.4 34.5 - - - +
45B ALA 3.4 15.0 - - - +
46B LYS* 4.3 26.7 - - + +
59B GLU* 4.9 4.7 - - - +
61B GLY* 1.3 73.9 - - - +
63B GLY* 1.3 62.7 + - - +
80B MET* 4.2 1.3 - - - -
81B ARG 4.2 1.6 - - - -
82B ARG* 3.4 5.8 - - - +
83B GLU* 2.9 48.3 + - + +
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Residues in contact with GLY 63 (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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44B ARG* 4.1 8.3 - - - -
45B ALA 2.9 32.3 + - - +
62B ILE* 1.3 78.9 - - - +
64B ASN* 1.3 65.5 + - - -
80B MET* 3.3 10.5 - - - +
81B ARG 3.1 12.1 - - - -
83B GLU* 4.3 9.9 - - - -
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Residues in contact with ASN 64 (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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42B CYS* 4.5 21.8 - - - -
43B ASN* 3.6 4.4 - - - +
44B ARG* 3.2 31.6 + - - +
63B GLY* 1.3 70.1 - - - -
65B VAL* 1.3 60.6 + - - +
66B LYS* 4.5 14.3 - - - +
79B LEU 3.8 0.7 - - - +
80B MET* 3.3 5.0 - - - -
81B ARG* 3.0 33.8 + - + +
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Residues in contact with VAL 65 (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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41B PHE* 3.7 11.2 - - + +
42B CYS* 3.3 4.7 - - - -
43B ASN 2.9 31.6 + - - +
45B ALA* 3.4 32.8 - - + -
64B ASN* 1.3 72.2 - - - +
66B LYS* 1.3 65.4 + - - +
78B LEU* 4.1 31.6 - - + -
79B LEU 3.7 4.3 - - - +
80B MET* 3.5 19.3 - - + -
129B ILE* 3.4 24.0 - - + -
131B PHE* 4.7 0.9 - - + -
140B PHE* 4.3 7.0 - - + -
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Residues in contact with LYS 66 (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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34B GLU* 3.1 34.6 + - - +
39B GLU* 3.7 23.9 + - - +
41B PHE 3.0 11.2 - - - +
42B CYS* 4.1 16.8 - - - -
64B ASN* 4.5 16.2 - - - +
65B VAL* 1.3 81.4 - - - +
67B ILE* 1.3 63.5 + - - +
68B LEU* 3.9 17.0 + - + -
77B ARG 3.9 0.2 - - - +
78B LEU* 3.5 6.1 - - - +
79B LEU* 2.8 43.6 + - + +
81B ARG* 4.9 13.7 - - - +
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Residues in contact with ILE 67 (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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40B PHE* 2.5 45.3 + - + -
41B PHE* 3.0 37.8 + - + -
66B LYS* 1.3 76.8 - - - +
68B LEU* 1.3 60.3 + - - +
76B ILE* 3.6 24.5 - - + -
77B ARG 3.5 2.9 - - - +
78B LEU* 4.6 4.0 - - + -
94B ILE* 3.9 17.7 - - + -
140B PHE* 4.3 21.1 - - + -
143B LYS* 3.9 5.4 - - + +
144B PHE* 3.7 31.6 - - + +
147B ALA* 4.3 6.5 - - + -
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Residues in contact with LEU 68 (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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34B GLU* 3.6 37.2 - - + +
37B GLU* 3.4 33.9 - - + +
38B GLU 3.3 4.5 - - - +
39B GLU* 3.6 32.1 - - + -
40B PHE* 5.1 0.4 - - - -
66B LYS* 3.9 16.8 - - + +
67B ILE* 1.3 84.6 - - - +
69B ARG* 1.3 59.6 + - - +
70B HIS 4.1 0.6 + - - -
75B LYS 3.7 1.0 - - - +
76B ILE* 3.1 7.0 - - - -
77B ARG* 2.9 41.6 + - + +
79B LEU* 3.8 20.4 - - + -
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Residues in contact with ARG 69 (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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37B GLU* 3.9 2.9 - - - -
38B GLU* 2.9 52.9 + - + +
40B PHE* 3.1 43.3 - - + -
68B LEU* 1.3 73.2 - - - +
70B HIS* 1.3 83.5 + - - +
71B LYS* 3.4 8.4 + - - +
74B GLY* 3.5 26.0 - - - +
75B LYS 3.4 3.4 - - - -
76B ILE* 3.6 17.9 - - + +
150B ILE* 4.9 14.6 - - - +
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Residues in contact with HIS 70 (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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36B ASP* 2.8 50.3 - - + +
37B GLU* 3.7 12.9 - - + +
69B ARG* 1.3 77.6 + - - +
71B LYS* 1.3 69.2 + - - +
72B THR* 3.9 16.1 + - - -
73B SER* 2.8 40.8 + - - +
74B GLY* 3.1 21.5 + - - -
75B LYS* 2.8 16.8 + - + +
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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