Contacts of the strand formed by residues 64 - 71 (chain A) in PDB entry 2QU7
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 SER 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 1.3 73.3 - - - +
65A ASN* 1.3 54.5 + - - +
66A ILE* 3.0 10.9 + - - +
118A GLN 4.0 4.4 + - - -
119A ASN* 2.8 9.7 + - - +
120A VAL* 3.6 16.1 + - - -
121A SER* 2.5 32.5 + - - -
114B THR* 5.0 1.8 - - - -
118B GLN* 2.9 39.7 + - - -
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Residues in contact with ASN 65 (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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63A ARG 4.0 0.2 + - - -
64A SER* 1.3 70.1 - - - +
66A ILE* 1.3 52.9 + - - +
93A HIS* 3.5 16.9 + - - +
94A LEU* 3.2 22.2 - - + +
95A HIS* 2.8 48.1 + - - -
121A SER* 3.9 0.2 - - - -
114B THR* 2.7 47.4 + - - +
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Residues in contact with ILE 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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64A SER* 3.0 10.0 + - - +
65A ASN* 1.3 79.6 - - - +
67A ILE* 1.3 75.4 + - - +
68A ALA* 4.4 2.5 - - + +
95A HIS* 3.2 15.7 - - + +
97A ALA* 4.3 14.4 - - + -
115A PHE* 5.5 4.0 - - + -
120A VAL* 3.5 20.0 - - + +
121A SER* 2.9 28.3 + - - -
111B LEU* 6.1 0.7 - - + -
114B THR* 3.2 32.8 - - + -
115B PHE* 3.5 22.9 - - + -
118B GLN* 3.2 29.2 - - - +
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Residues in contact with ILE 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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66A ILE* 1.3 79.3 - - - +
68A ALA* 1.3 65.1 + - - +
69A PHE 3.8 0.5 + - - -
89A CYS* 3.4 33.9 - - + -
94A LEU* 4.0 30.1 - - + -
95A HIS 2.7 11.0 + - - +
96A VAL* 3.3 13.0 - - + -
97A ALA 2.9 26.7 + - - +
121A SER* 4.7 1.6 - - - -
122A ALA* 3.5 17.5 - - + +
124A ILE* 4.0 31.4 - - + -
309A ILE* 4.2 11.4 - - + -
313A ILE* 4.3 13.2 - - + -
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Residues in contact with ALA 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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66A ILE* 4.1 2.6 - - + +
67A ILE* 1.3 74.2 - - - +
69A PHE* 1.3 55.2 + - - +
70A ILE* 3.9 2.0 - - + -
97A ALA* 3.5 4.7 - - - -
115A PHE* 3.5 51.6 - - + -
120A VAL* 4.7 3.6 - - + +
122A ALA 2.9 13.8 + - - +
123A ILE* 3.3 9.2 - - + +
124A ILE* 2.7 34.7 + - - +
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Residues in contact with PHE 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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67A ILE 3.8 0.4 + - - -
68A ALA* 1.3 71.3 - - - +
70A ILE* 1.3 61.7 + - - +
71A VAL* 3.4 25.6 - - + -
78A PHE* 3.5 27.6 - + - -
81A VAL* 4.7 2.9 - - + -
82A LEU* 3.9 26.9 - - + -
85A ILE* 4.4 11.7 - - + -
96A VAL* 3.8 20.2 - - + -
97A ALA 2.8 9.3 + - - +
98A VAL* 3.2 13.3 - - + +
99A ALA 3.1 23.0 + - - -
124A ILE* 3.5 34.5 - - + -
126A VAL* 3.7 26.5 - - + -
146A LEU* 4.2 16.4 - - + -
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Residues in contact with ILE 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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68A ALA* 4.8 0.2 - - + -
69A PHE* 1.3 74.8 - - - +
71A VAL* 1.3 66.6 + - - +
99A ALA 3.3 10.5 - - - +
101A SER* 4.7 9.4 - - - +
108A GLN* 4.8 7.4 - - + +
111A LEU* 4.2 18.2 - - + -
112A ILE* 3.8 33.0 - - + +
115A PHE* 4.1 31.2 - - + -
123A ILE* 3.8 22.0 - - + -
124A ILE 3.0 8.9 + - - +
125A LEU* 3.9 20.0 - - + -
126A VAL* 2.8 35.3 + - - +
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Residues in contact with VAL 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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69A PHE* 3.4 44.4 - - + -
70A ILE* 1.3 76.2 - - - +
72A PRO* 1.3 69.3 - - + +
73A ASP 3.7 16.6 - - - +
78A PHE* 4.0 16.2 - - + -
98A VAL* 3.8 22.7 - - + -
99A ALA 3.0 9.8 + - - +
100A SER* 3.1 17.1 - - - -
101A SER* 2.9 25.7 + - - -
126A VAL* 4.3 2.2 - - + -
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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