Contacts of the strand formed by residues 39 - 56 (chain B) in PDB entry 2Q53
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 ALA 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B SER 3.3 4.9 + - - +
38B ALA* 1.3 72.7 - - - +
40B PHE* 1.3 67.0 + - - +
41B PHE 3.2 0.2 + - - -
84B TRP* 3.3 5.9 - - - -
85B LYS* 2.7 54.3 + - + +
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Residues in contact with PHE 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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28B THR* 6.0 1.3 - - + +
39B ALA* 1.3 73.3 - - - +
41B PHE* 1.3 75.5 + - - +
42B CYS* 3.8 19.1 - - - -
43B VAL* 4.1 11.2 - - + -
82B VAL* 3.6 26.2 - - + -
84B TRP* 3.3 24.6 - + + -
85B LYS* 5.5 0.6 - - - +
150B ASN* 3.1 45.3 - - + +
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Residues in contact with PHE 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 4.1 26.0 - - + -
39B ALA 3.2 1.2 + - - -
40B PHE* 1.3 87.0 - - - +
42B CYS* 1.3 91.6 + - + +
83B VAL* 2.9 37.7 + - + +
84B TRP* 4.1 8.1 - - - +
85B LYS* 4.1 22.0 - - + +
120B ILE* 4.1 27.4 - - + -
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Residues in contact with CYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.8 15.6 - - - -
41B PHE* 1.3 107.9 - - + +
43B VAL* 1.3 61.9 + - - +
44B ALA* 4.6 0.7 - - - -
82B VAL* 3.6 1.6 - - - -
83B VAL* 2.7 47.0 + - - +
114B THR* 3.5 31.0 - - + -
120B ILE* 4.8 2.2 - - - -
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Residues in contact with VAL 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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40B PHE* 4.1 15.1 - - + -
42B CYS* 1.3 85.0 - - - +
44B ALA* 1.3 65.0 + - - +
80B TRP* 3.9 23.1 - - + -
81B GLY 3.5 10.3 - - - +
82B VAL* 4.7 2.5 - - + -
114B THR* 3.7 13.7 - - - -
115B GLN* 4.5 13.4 + - - +
150B ASN 3.4 26.7 - - - +
151B GLY 3.9 6.7 - - - +
152B LEU* 4.3 16.6 - - + -
153B PRO* 4.3 11.9 - - + -
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B PHE* 3.6 4.3 - - + -
42B CYS* 4.6 3.4 - - - -
43B VAL* 1.3 77.1 - - - +
45B ARG* 1.3 60.5 + - - +
80B TRP* 3.2 12.5 - - - -
81B GLY 2.8 34.4 + - - -
83B VAL* 3.5 24.9 - - + -
112B VAL* 3.6 21.3 - - + -
113B ALA 3.6 12.6 - - - +
114B THR* 4.4 2.0 - - + +
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Residues in contact with ARG 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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44B ALA* 1.3 73.3 - - - +
46B LEU* 1.3 66.5 + - - +
47B GLN* 2.9 41.9 + - - +
78B GLU* 3.6 24.7 - - + -
79B VAL 3.7 2.9 - - - -
80B TRP* 3.5 45.9 - - + +
112B VAL* 3.3 8.3 - - - +
113B ALA* 2.9 53.4 + - - +
114B THR 5.4 2.4 + - - -
117B GLY* 6.0 2.0 - - - -
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Residues in contact with LEU 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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20B PHE* 3.8 26.2 - - + -
45B ARG* 1.3 74.0 - - - +
47B GLN* 1.3 63.8 + - - +
49B PHE* 3.4 41.3 + - + -
71B ILE* 3.5 31.4 - - + -
78B GLU* 3.4 1.9 - - - -
79B VAL* 2.6 42.3 + - + +
110B VAL* 4.4 14.4 - - + -
111B LYS 4.2 16.8 - - - +
112B VAL* 4.0 7.4 - - + +
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Residues in contact with GLN 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 ARG* 2.9 39.3 + - - +
46B LEU* 1.3 78.9 - - - +
48B ASP* 1.3 93.6 + - - +
49B PHE* 3.3 11.8 + - - -
76B GLY* 3.9 11.9 + - - -
77B ASP 3.0 26.4 + - - -
78B GLU* 3.9 15.4 + - - +
111B LYS 5.5 1.0 + - - -
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Residues in contact with ASP 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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101A LYS 4.5 12.5 - - - +
102A SER 6.3 1.1 - - - -
103A GLY* 5.7 7.3 - - - +
47B GLN* 1.3 91.9 + - - +
49B PHE* 1.3 56.1 + - + +
73B GLN* 3.4 6.9 - - - +
74B SER 2.6 36.4 + - - -
75B PRO* 3.2 14.9 - - + +
76B GLY 2.8 28.1 + - - -
77B ASP 2.6 17.1 + - - -
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Residues in contact with PHE 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 3.9 18.8 - - + -
46B LEU* 3.4 45.3 - - + +
47B GLN 3.2 9.0 - - - -
48B ASP* 1.3 81.2 - - + +
50B LYS* 1.3 59.3 + - - +
71B ILE* 3.7 27.1 - - + -
72B PHE 3.2 18.2 - - - -
73B GLN* 3.5 31.4 - - + -
74B SER 4.7 0.4 - - - -
77B ASP* 3.3 2.9 - - - -
78B GLU 3.2 29.6 + - - -
79B VAL* 3.8 6.7 - - + -
110B VAL* 4.7 7.2 - - + -
126B LEU* 4.1 17.0 - - + -
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Residues in contact with LYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 1.3 74.9 - - - +
51B LEU* 1.3 76.4 + - - +
52B ASP 3.8 0.2 + - - -
71B ILE* 3.3 2.1 - - - -
72B PHE* 2.7 71.0 + - + +
74B SER* 4.1 7.9 - - - +
77B ASP* 4.0 23.8 + - + +
78B GLU 4.9 1.6 - - - -
79B VAL* 3.9 3.1 - - - -
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Residues in contact with LEU 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TYR* 4.0 19.3 - - + +
50B LYS* 1.3 90.8 - - - +
52B ASP* 1.3 70.1 + - - +
53B PHE* 3.6 27.1 - - + -
69B ALA* 3.8 20.6 - - + -
70B THR 3.2 20.0 - - - +
71B ILE* 4.1 3.4 - - - -
78B GLU 5.0 0.8 + - - -
79B VAL* 3.4 17.0 - - + +
143B ILE* 6.0 0.2 - - + -
156B TYR* 3.8 20.2 - - + +
160B LEU* 4.1 17.0 - - + -
163B ILE* 4.7 2.2 - - + -
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Residues in contact with ASP 52 (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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51B LEU* 1.3 79.1 - - - +
53B PHE* 1.3 82.2 + - - +
69B ALA* 3.4 4.7 - - - -
70B THR* 2.7 42.2 + - + +
72B PHE* 4.0 17.7 - - + -
130B TYR* 3.1 33.5 + - - +
132B SER* 3.2 16.4 + - - -
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Residues in contact with PHE 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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51B LEU* 3.6 35.9 - - + -
52B ASP* 1.3 85.8 + - - +
54B GLY* 1.3 58.4 + - - +
67B GLY 3.7 7.2 - - - +
68B ILE 3.3 4.7 - - - +
69B ALA* 3.6 20.0 - - + -
70B THR* 5.0 0.4 - - - -
130B TYR* 5.0 2.0 - - - -
132B SER* 3.4 10.2 - - - -
133B ALA 2.9 32.3 + - - +
134B PRO* 4.8 0.2 - - + -
135B PRO* 3.7 31.6 - - + -
139B TYR* 3.7 6.1 - + - -
140B LYS* 6.1 0.9 - - - -
143B ILE* 3.6 31.9 - - + -
163B ILE* 4.1 28.7 - - + -
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Residues in contact with GLY 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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53B PHE* 1.3 76.7 - - - +
55B ASN* 1.3 61.8 - - - +
56B SER 3.7 2.7 + - - -
66B GLY 4.9 0.2 - - - +
67B GLY* 3.5 7.5 - - - -
68B ILE* 3.1 35.2 + - - +
127B MSE 4.0 6.6 - - - +
130B TYR* 4.3 5.2 - - - -
131B GLU 3.3 12.1 - - - -
132B SER* 4.0 0.9 - - - -
133B ALA* 3.4 10.6 + - - -
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Residues in contact with ASN 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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54B GLY* 1.3 74.6 - - - +
56B SER* 1.3 66.1 + - - +
57B GLN 3.3 0.3 + - - -
58B GLY* 2.9 16.9 + - - -
59B LYS 3.2 22.5 - - - +
60B THR* 3.2 34.8 + - - +
61B SER 4.1 0.3 + - - -
66B GLY 4.1 11.4 - - - +
130B TYR* 3.8 1.8 - - - -
131B GLU* 2.8 31.8 + - + +
132B SER 5.2 0.2 + - - -
133B ALA* 3.7 20.3 - - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A GLN* 5.4 0.2 + - - -
54B GLY 3.7 4.8 + - - -
55B ASN* 1.3 66.9 - - - +
57B GLN* 1.3 64.2 + - - +
59B LYS* 2.7 36.1 + - - +
68B ILE* 5.5 4.8 - - - +
103B GLY 3.8 4.0 + - - -
104B MSE 2.9 49.5 + - - +
127B MSE 3.4 20.5 - - - +
129B ASN 3.5 10.9 + - - -
130B TYR* 3.8 4.9 - - - -
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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