Contacts of the strand formed by residues 70 - 76 (chain A) in PDB entry 1Q90
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 ASN 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASP* 4.9 6.1 + - - +
69A LEU* 1.3 82.6 + - - +
71A VAL* 1.3 63.6 + - - +
117A PRO* 4.1 8.6 - - + +
118A VAL* 3.0 18.8 - - - +
119A PRO* 3.5 21.4 - - - +
154A ARG* 3.2 2.4 - - - -
155A GLY 3.1 23.2 + - - -
900A HEC 2.5 40.9 + - + +
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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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51A LEU* 3.8 15.9 - - + -
53A TYR* 4.9 2.5 - - + -
70A ASN* 1.3 72.9 - - - +
72A GLY* 1.3 59.3 + - - +
115A VAL* 5.3 0.2 - - - +
116A GLY* 3.5 3.1 - - - -
117A PRO* 3.4 4.0 - - - +
118A VAL* 2.7 51.7 + - + +
120A GLY* 3.4 22.7 - - - +
123A TYR 3.4 23.8 - - - +
124A SER* 4.8 2.7 - - - -
126A MET* 3.9 7.9 - - + -
153A ASN 3.3 7.0 - - - +
154A ARG* 3.2 27.6 - - + -
900A HEC 3.3 6.1 - - - -
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Residues in contact with GLY 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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2A PRO* 4.6 0.7 - - - -
51A LEU* 3.5 4.7 - - - +
71A VAL* 1.3 75.8 - - - +
73A MET* 1.3 66.1 + - - +
115A VAL* 3.2 17.5 - - - -
116A GLY* 4.2 0.9 - - - -
126A MET* 4.9 0.4 - - - -
153A ASN 3.0 27.3 + - - +
900A HEC 3.5 23.7 - - - +
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Residues in contact with MET 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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49A ILE* 3.7 20.6 - - + -
51A LEU* 4.9 0.2 - - + -
72A GLY* 1.3 74.9 - - - +
74A VAL* 1.3 64.6 + - - +
75A LEU* 3.6 18.2 - - + +
102A TYR* 4.0 14.8 - - + -
113A LEU* 3.2 26.9 - - + +
114A VAL* 3.1 43.6 - - - +
115A VAL* 3.1 31.2 + - + +
126A MET* 4.3 4.7 - - + -
128A VAL* 5.3 3.1 - - + -
150A PHE* 3.5 20.4 - - + -
151A GLY 3.2 15.3 - - - +
152A GLY* 4.3 0.2 - - - -
900A HEC 3.5 12.5 - - - +
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Residues in contact with VAL 74 (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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12A PRO* 4.3 16.2 - - + -
19A ILE* 3.8 26.2 - - + -
21A CYS* 4.2 9.6 - - - -
73A MET* 1.3 77.2 - - - +
75A LEU* 1.3 60.8 + - - +
76A ILE* 4.1 5.8 - - + -
105A TYR* 4.6 1.6 - - + -
112A ILE* 3.6 27.1 - - + -
113A LEU 3.2 5.4 - - - +
114A VAL* 4.0 9.2 - - + -
149A TYR 4.0 0.9 - - - +
150A PHE* 3.6 1.9 - - - -
151A GLY* 2.7 51.9 + - - +
900A HEC 4.1 11.0 - - + -
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Residues in contact with LEU 75 (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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33A ILE* 3.9 15.0 - - + -
47A ALA* 4.1 13.9 - - + -
49A ILE* 5.5 1.1 - - + -
73A MET* 3.6 14.6 - - + -
74A VAL* 1.3 73.7 - - - +
76A ILE* 1.3 65.7 + - - +
77A LEU* 3.5 25.1 + - + +
111A ASN 3.8 0.7 - - - +
112A ILE* 3.4 4.4 - - - +
113A LEU* 2.7 40.4 + - + +
128A VAL* 4.6 14.8 - - + -
130A ILE* 3.8 18.8 - - + -
148A ILE* 3.2 31.0 - - + -
149A TYR 3.6 5.8 - - - +
150A PHE* 4.4 5.6 - - + -
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Residues in contact with ILE 76 (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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12A PRO* 4.2 13.0 - - + -
13A ARG* 3.8 25.1 - - + -
19A ILE* 3.8 28.9 - - + -
74A VAL* 4.3 7.0 - - + +
75A LEU* 1.3 75.0 - - - +
77A LEU* 1.3 68.5 + - - +
111A ASN* 4.1 3.6 - - - +
112A ILE* 4.1 30.5 - - + +
147A PRO 4.5 0.2 - - - +
148A ILE* 3.4 9.5 - - - +
149A TYR* 2.7 55.4 + - + +
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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