Contacts of the strand formed by residues 41 - 57 (chain B) in PDB entry 1QZG
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 THR 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLN* 3.2 24.8 + - + +
39B LYS* 3.7 12.8 - - + +
40B ASN* 1.3 80.6 - - - +
42B ILE* 1.3 66.3 + - - +
43B VAL* 4.0 6.4 + - - +
110B ILE 3.6 0.9 - - - +
111B THR* 3.3 2.5 - - - -
112B LEU* 2.6 48.1 + - - +
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Residues in contact with ILE 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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41B THR* 1.3 76.0 - - - +
43B VAL* 1.3 70.0 + - - +
109B GLN* 4.0 28.3 - - + +
110B ILE 3.4 4.7 - - - +
111B THR* 4.0 12.8 - - + +
124B LYS* 3.6 45.5 - - + +
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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
----------------------------------------------------------
28B GLN* 4.4 23.8 - - + +
33B SER* 4.7 0.2 - - - +
41B THR* 4.3 9.2 - - - +
42B ILE* 1.3 81.9 - - - +
44B ASN* 1.3 70.0 + - - +
45B LEU* 3.7 27.8 - - + -
109B GLN* 3.2 8.1 + - - -
110B ILE* 2.9 42.1 + - - +
112B LEU* 4.0 30.7 - - + -
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Residues in contact with ASN 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 4.1 15.7 - - + +
26B THR* 3.1 28.6 + - - +
27B PHE* 3.5 16.5 - - + -
28B GLN 3.2 24.5 + - - +
43B VAL* 1.3 76.6 - - - +
45B LEU* 1.3 68.3 - - - +
107B LEU 3.3 8.3 - - - +
108B HIS* 2.8 36.4 + - - -
109B GLN* 3.1 12.3 + - - +
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Residues in contact with LEU 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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27B PHE* 3.5 6.8 - - - -
28B GLN 3.6 19.1 - - - +
30B ILE* 4.5 10.5 - - + -
33B SER* 3.6 18.8 - - - +
43B VAL* 3.7 15.5 - - + -
44B ASN* 1.3 83.7 - - - +
46B PHE* 1.3 61.0 + - - +
47B GLY 4.3 0.4 - - - -
71B LEU* 3.9 13.9 - - + -
83B LEU* 3.8 13.0 - - + -
85B ILE* 3.5 30.1 - - + -
105B LEU 4.5 0.7 - - - -
106B LEU* 3.4 1.7 - - - -
107B LEU* 2.7 41.8 + - + +
110B ILE* 4.3 23.1 - - + -
112B LEU* 4.8 0.2 - - + -
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B TYR* 3.3 22.8 + - - +
22B ILE* 4.6 5.6 - - + -
27B PHE* 3.6 18.2 - + + +
28B GLN 5.3 1.4 + - - -
30B ILE* 5.0 3.4 - - - +
45B LEU* 1.3 76.5 - - - +
47B GLY* 1.3 59.2 + - - +
71B LEU* 4.6 0.9 - - - -
73B ASP* 4.2 12.5 - - - +
104B PRO* 4.5 3.6 - - + -
105B LEU 3.4 13.7 - - - -
106B LEU* 3.7 24.0 - - + -
132B TRP* 3.7 31.4 - + - -
158B GLU* 3.7 30.7 - - + -
161B PHE* 3.7 24.6 - + + -
162B ALA* 4.0 13.0 - - + -
165B LEU* 3.7 18.0 - - + +
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Residues in contact with GLY 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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30B ILE* 5.3 1.1 - - - -
46B PHE* 1.3 76.0 - - - +
48B ILE* 1.3 64.0 + - - +
71B LEU* 3.3 16.8 - - - +
72B TRP 3.2 13.7 - - - -
73B ASP* 4.5 1.3 - - - -
104B PRO* 3.3 5.2 - - - +
105B LEU 2.8 32.8 + - - -
165B LEU* 4.0 9.2 - - - -
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Residues in contact with ILE 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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47B GLY* 1.3 73.7 - - - +
49B VAL* 1.3 70.5 + - - +
50B LYS* 3.2 2.5 + - + -
71B LEU* 3.5 3.7 - - - +
72B TRP* 2.7 50.6 + - + +
102B GLY* 3.4 31.2 - - - +
103B GLN 3.7 1.1 - - - -
104B PRO* 3.5 32.5 - - + -
165B LEU* 3.6 36.1 - - + +
166B ASN* 3.7 10.3 - - - +
169B TRP* 3.9 22.7 - - + -
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Residues in contact with VAL 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ILE* 1.3 70.3 - - - +
50B LYS* 1.3 58.0 + - - +
51B ASP 3.5 27.4 - - - +
52B PHE* 3.9 21.5 - - + -
69B VAL* 5.0 3.6 - - + -
70B TYR 3.7 4.7 - - - +
71B LEU* 4.4 2.5 - - + -
98B ILE* 4.1 23.8 - - + -
100B GLN 4.4 7.0 - - - +
101B VAL* 2.9 8.6 - - - +
102B GLY 2.8 27.6 + - - +
103B GLN* 2.9 29.4 + - + +
105B LEU* 4.1 23.6 - - + -
131B LEU* 5.0 0.4 - - + -
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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
----------------------------------------------------------
48B ILE* 3.2 1.4 + - - -
49B VAL* 1.3 73.5 - - - +
51B ASP* 1.3 64.5 + - - +
70B TYR 2.7 9.1 + - - +
72B TRP* 3.7 40.4 - - + +
78B THR* 3.4 27.7 + - - +
80B SER 3.4 16.4 - - - +
81B ILE* 3.0 36.6 - - + +
101B VAL* 3.5 21.2 - - + +
169B TRP* 4.4 22.2 - - + +
173B THR* 5.4 2.0 + - - -
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Residues in contact with ASP 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 2.8 23.8 + - - -
139A SER* 4.8 3.2 + - - -
141A ASP* 2.8 28.9 - - - +
49B VAL* 3.5 6.5 - - - +
50B LYS* 1.3 80.3 - - - +
52B PHE* 1.3 75.1 + - - +
69B VAL* 3.5 1.0 - - - -
70B TYR* 2.9 50.3 + - + -
81B ILE* 4.2 10.0 - - + +
101B VAL* 4.1 9.2 - - - +
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Residues in contact with PHE 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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52A PHE* 5.7 0.4 - + - -
98A ILE 5.6 0.4 - - - -
99A LYS* 3.1 64.4 + - + -
49B VAL* 3.9 14.1 - - + -
51B ASP* 1.3 87.3 + - - +
53B THR* 1.3 68.2 + - - +
54B PRO* 4.0 27.6 - - + -
67B THR* 5.7 0.9 - - - +
68B THR 3.1 14.6 - - - +
69B VAL* 4.2 0.2 - - + -
70B TYR* 5.1 2.7 - - - -
98B ILE* 3.8 42.8 - - + -
99B LYS 3.8 14.6 - - - -
100B GLN* 3.8 19.1 - - - -
101B VAL* 4.0 10.8 - - + -
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Residues in contact with THR 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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99A LYS* 5.3 0.8 + - - -
141A ASP* 5.2 3.6 + - - -
144A CYS* 4.8 12.3 - - + -
145A PRO* 5.2 5.2 - - + -
52B PHE* 1.3 80.3 + - - +
54B PRO* 1.3 76.1 - - + +
56B ARG* 3.8 21.8 - - - +
67B THR* 2.7 28.3 + - - -
68B THR* 2.9 33.0 + - - +
70B TYR* 5.6 2.4 - - - -
5D A 5.3 2.5 - - - +
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Residues in contact with PRO 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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54A PRO* 6.5 1.1 - - + -
97A VAL* 3.8 28.0 - - + -
98A ILE 4.3 12.1 - - - +
99A LYS* 4.4 5.2 - - + -
144A CYS* 3.9 20.6 - - - -
52B PHE* 4.0 25.3 - - + +
53B THR* 1.3 97.2 - - + +
55B SER* 1.3 67.1 + - - +
56B ARG* 3.7 8.1 + - - +
66B VAL 4.1 2.9 - - - +
67B THR* 4.3 0.9 - - - +
98B ILE 5.8 1.3 - - - +
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Residues in contact with SER 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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97A VAL* 5.8 2.4 - - - +
53B THR 3.5 0.8 + - - -
54B PRO* 1.3 79.8 - - - +
56B ARG* 1.3 63.4 + - - +
65B TRP* 4.8 1.2 - - - -
66B VAL 3.3 11.4 - - - -
67B THR* 3.7 16.8 + - - -
93B ASN* 3.6 33.7 + - - -
95B LEU* 4.1 6.3 + - - +
96B PRO 3.7 14.2 + - - -
97B VAL* 5.3 4.2 - - - +
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Residues in contact with ARG 56 (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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145A PRO* 4.3 28.7 - - - +
53B THR* 3.8 24.4 - - - +
54B PRO 4.4 4.4 + - - +
55B SER* 1.3 78.4 - - - +
57B GLN* 1.3 70.9 + - - +
59B LEU* 5.9 4.8 - - - +
65B TRP* 3.7 15.3 - - - -
66B VAL* 2.8 39.9 + - + +
67B THR* 6.0 0.2 - - - +
68B THR* 5.9 0.2 + - - -
5D A 3.0 48.2 + - - -
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Residues in contact with GLN 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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56B ARG* 1.3 83.1 + - - +
58B SER* 1.3 68.8 + - - +
59B LEU* 3.5 11.6 + - - +
63B LYS* 3.4 33.9 + - - +
64B ASP 3.8 2.0 - - - -
65B TRP* 3.7 46.2 - - + +
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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