Contacts of the strand formed by residues 65 - 73 (chain A) in PDB entry 1QM4
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 MET 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A VAL* 6.0 2.9 - - + +
61A CYS* 3.2 6.5 - - - +
62A LYS* 2.8 51.6 + - + +
63A THR 3.1 1.3 - - - +
64A GLY* 1.3 79.9 - - - +
66A VAL* 1.3 62.7 + - - +
67A LEU* 4.3 16.8 - - + -
100A PHE* 4.2 1.2 - - - -
106A ASN* 3.4 17.7 - - + +
108A LEU* 4.9 19.7 - - + -
67B LEU* 5.6 11.2 - - + -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ILE* 5.7 0.2 - - + -
38A ILE* 3.8 15.5 - - + -
59A THR* 3.7 24.7 - - + -
60A VAL 3.5 3.1 - - - +
61A CYS* 4.0 6.3 - - + -
65A MET* 1.3 79.0 - - - +
67A LEU* 1.3 63.8 + - - +
68A LEU* 5.0 1.3 - - + +
84A VAL* 3.8 19.1 - - + -
88A ILE* 4.1 14.4 - - + -
100A PHE* 3.7 28.9 - - + -
105A CYS* 4.5 2.5 - - - -
106A ASN 2.7 13.7 + - - +
107A VAL* 3.3 5.6 - - + +
108A LEU* 2.8 29.2 + - - +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 3.3 7.0 - - - -
60A VAL* 2.8 57.7 + - + +
65A MET* 4.3 13.2 - - + -
66A VAL* 1.3 72.3 - - - +
68A LEU* 1.3 72.5 + - - +
69A CYS* 3.9 18.2 + - - -
108A LEU* 3.4 28.0 - - + +
110A ALA* 3.9 17.3 - - + -
60B VAL* 5.9 4.3 - - + -
62B LYS* 4.7 9.9 - - + -
65B MET* 5.6 9.9 - - + -
260B ALA* 5.9 0.7 - - + -
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Residues in contact with LEU 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ILE* 5.0 1.6 - - + -
42A VAL* 4.1 15.0 - - + -
57A CYS* 4.2 18.6 - - + -
58A GLU 3.7 8.5 - - - +
59A THR* 4.2 13.2 - - + +
66A VAL* 4.1 1.7 + - + +
67A LEU* 1.3 71.8 - - - +
69A CYS* 1.3 72.3 + - - +
80A TYR* 3.5 41.1 - - + -
84A VAL* 4.5 14.4 - - + -
107A VAL* 5.7 1.1 - - + -
108A LEU 3.1 10.6 + - - +
109A VAL* 4.2 13.0 - - + -
110A ALA* 2.8 33.3 + - - +
111A LEU* 3.5 15.8 + - + -
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Residues in contact with CYS 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A CYS* 3.2 9.4 - - - +
58A GLU* 2.9 32.9 + - + +
60A VAL* 5.3 2.9 - - - -
67A LEU* 4.1 18.8 - - - -
68A LEU* 1.3 76.7 - - - +
70A GLY* 1.3 60.4 + - - +
110A ALA 4.4 6.3 - - - -
111A LEU* 3.4 7.3 - - - +
62B LYS* 3.2 39.7 - - - -
259B ASP 4.0 15.9 - - - +
260B ALA* 3.8 13.0 - - - -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A ALA 3.2 11.7 - - - -
57A CYS* 4.0 1.3 - - - -
69A CYS* 1.3 79.4 - - - +
71A GLU* 1.3 59.9 + - - -
110A ALA 4.5 2.1 + - - +
111A LEU* 3.3 10.8 - - - +
112A GLU* 2.9 31.2 + - - +
259B ASP* 3.1 25.4 + - - +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A LYS 4.2 0.9 - - - +
55A VAL 4.2 0.2 - - - -
56A ALA* 3.0 27.0 + - + +
70A GLY* 1.3 71.2 - - - -
72A ILE* 1.3 67.1 + - - +
73A THR* 4.2 3.2 + - - -
112A GLU* 3.7 18.9 - - + +
114A GLN* 2.5 47.3 + - - +
259B ASP* 3.2 11.1 + - - +
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Residues in contact with ILE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.1 9.4 - - + -
46A HIS* 3.3 30.5 - - + +
54A LYS 3.1 12.1 - - - +
55A VAL* 3.7 13.2 - - + -
56A ALA 3.4 22.2 - - - +
57A CYS* 4.2 6.3 - - + -
70A GLY 4.1 0.2 - - - -
71A GLU* 1.3 81.8 - - - +
73A THR* 1.3 60.3 + - - +
80A TYR* 3.1 28.9 - - + +
111A LEU* 3.4 20.2 - - + -
112A GLU 3.1 8.5 + - - -
113A GLN* 3.3 9.7 - - + +
114A GLN* 3.2 22.4 + - - +
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASN 4.6 0.5 - - - +
53A ALA* 3.7 1.2 - - - -
54A LYS* 2.8 44.3 + - + -
71A GLU* 4.2 2.8 + - - -
72A ILE* 1.3 68.9 - - - +
74A SER* 1.3 61.2 + - - +
114A GLN* 3.2 32.9 + - + +
115A SER 4.5 5.4 - - - -
116A PRO* 3.9 30.3 - - + +
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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