Contacts of the strand formed by residues 94 - 101 (chain A) in PDB entry 1QST
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 HIS 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A ASN* 6.1 1.4 - - - +
88A LEU* 3.1 49.9 - - + +
89A VAL 4.6 6.4 - - - +
91A ASP* 2.8 42.0 + - + +
92A ARG 3.5 2.3 - - - +
93A HIS* 1.3 81.1 + - + +
95A GLU* 1.3 65.1 + - - +
111A CYS* 3.9 21.8 - - - -
112A PHE 3.3 10.1 - - - +
113A ARG* 3.6 31.6 - - + +
124A ALA* 4.1 12.2 - - + +
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Residues in contact with GLU 95 (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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53A ILE* 4.4 17.0 - - + +
54A LEU 4.8 3.8 - - - +
89A VAL 5.9 0.7 - - - -
93A HIS 4.6 5.7 - - - +
94A HIS* 1.3 79.0 - - - +
96A SER* 1.3 62.9 + - - +
111A CYS* 3.3 3.9 - - - -
112A PHE* 2.8 58.8 + - + +
114A GLN* 2.8 37.1 + - - +
116A LYS* 4.5 9.1 + - - -
148A HIS* 4.8 5.5 - - - -
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Residues in contact with SER 96 (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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53A ILE* 3.4 2.5 - - - -
54A LEU* 2.5 43.9 + - - +
66A LEU* 4.1 20.7 - - - +
69A LEU* 3.6 31.0 - - - +
89A VAL* 4.6 6.9 + - - +
95A GLU* 1.3 80.4 + - - +
97A MET* 1.3 56.4 + - - +
98A VAL 3.9 0.2 - - - -
110A ILE 3.1 6.1 - - - -
111A CYS* 3.8 15.2 - - - +
112A PHE* 4.2 3.1 - - - -
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Residues in contact with MET 97 (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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51A PHE* 4.2 18.8 - - + +
52A ASP 3.3 12.8 - - - +
53A ILE* 3.8 27.1 - - + -
96A SER* 1.3 72.1 - - - +
98A VAL* 1.3 62.5 + - - +
109A GLY* 3.1 3.3 - - - -
110A ILE* 2.9 34.8 + - + +
112A PHE* 4.0 6.3 - - + -
141A LEU* 3.9 23.2 - - + +
144A LYS* 3.8 27.4 - - + +
145A PHE* 3.8 31.2 - - + -
148A HIS* 3.8 20.2 - - + -
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Residues in contact with VAL 98 (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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50A ASP 3.4 1.2 - - - +
51A PHE* 3.3 6.6 - - - -
52A ASP* 2.8 46.2 + - + +
54A LEU* 3.5 41.3 - - + -
65A LEU 4.9 0.2 - - - +
69A LEU* 3.8 31.0 - - + -
96A SER* 3.9 0.4 - - - -
97A MET* 1.3 79.2 - - - +
99A ILE* 1.3 64.5 + - - +
100A LEU* 4.4 20.9 - - + +
106A VAL* 4.6 8.7 - - + -
108A GLY 3.5 9.2 - - - +
141A LEU* 5.0 0.2 - - - -
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Residues in contact with ILE 99 (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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49A LEU* 3.6 31.9 - - + -
50A ASP 3.5 3.6 - - - +
51A PHE* 3.7 18.6 - - + -
98A VAL* 1.3 71.3 - - - +
100A LEU* 1.3 60.5 + - - +
106A VAL* 3.4 4.2 - - - -
107A ILE* 3.0 47.7 + - + +
108A GLY* 2.9 25.2 + - - +
128A VAL* 4.4 8.3 - - + -
137A TYR* 4.1 21.1 - - + +
141A LEU* 3.9 34.8 - - + -
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Residues in contact with LEU 100 (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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49A LEU* 3.4 7.1 - - - -
50A ASP* 2.7 52.0 + - + +
52A ASP* 3.7 20.9 - - + +
54A LEU* 6.5 0.2 - - + -
61A ARG* 4.0 9.9 - - - +
65A LEU* 4.0 32.1 - - + -
98A VAL* 3.5 16.3 + - + -
99A ILE* 1.3 71.5 - - - +
101A LYS* 1.3 60.2 + - - +
102A ASN 3.9 1.4 + - - -
103A LYS* 3.8 33.4 + - - +
104A GLN 4.1 11.2 - - - -
105A LYS 3.8 0.2 - - - -
106A VAL* 4.2 10.5 - - + +
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Residues in contact with LYS 101 (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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49A LEU* 3.9 19.7 - - + +
99A ILE 3.8 0.4 + - - -
100A LEU* 1.3 71.8 - - - +
102A ASN* 1.3 86.4 + - - +
103A LYS 3.2 1.1 - - - -
104A GLN* 4.9 0.2 - - - +
105A LYS* 2.7 51.7 + - + +
107A ILE* 4.0 17.3 - - + -
132A GLU* 3.1 31.5 + - - +
137A TYR* 5.1 7.4 + - - +
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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