Contacts of the strand formed by residues 89 - 100 (chain B) in PDB entry 1Q4U
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 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B VAL* 3.2 29.5 + - + +
85B HIS* 3.6 10.0 + - - -
87B LYS* 3.7 15.5 - - + +
88B GLY* 1.3 84.5 - - - +
90B MET* 1.3 59.9 + - - +
120B SER 4.5 8.3 - - - +
146B VAL* 3.7 34.8 - - + +
147B ARG* 3.1 14.4 - - - +
148B PRO* 3.5 26.9 - - + -
149B ARG* 3.2 19.4 + - - +
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Residues in contact with MET 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A 4CA 3.9 32.1 - - + +
84B VAL* 4.6 0.2 - - - -
85B HIS* 5.9 0.4 - - - -
89B MET* 1.3 75.4 - - - +
91B ALA* 1.3 61.3 + - - +
92B VAL* 3.8 33.4 - - + -
145B ALA 4.0 8.5 - - - +
146B VAL* 3.3 5.5 - - - +
147B ARG* 2.6 57.0 + - + +
148B PRO 4.6 1.3 - - - +
149B ARG* 3.8 20.4 - - + +
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Residues in contact with ALA 91 (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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371A 4CA 5.0 1.2 - - - -
77B THR* 3.4 14.9 - - - +
80B THR* 3.7 31.0 - - + -
81B VAL* 4.0 23.6 - - + +
84B VAL* 4.0 11.8 - - + +
89B MET 4.4 0.4 + - - -
90B MET* 1.3 75.8 - - - +
92B VAL* 1.3 67.7 + - - +
144B ILE* 3.9 6.3 - - + -
145B ALA 3.2 5.6 - - - +
146B VAL* 4.5 0.4 - - + -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLN* 5.6 1.6 - - - +
62A LEU* 5.3 10.5 - - + -
371A 4CA 3.8 66.4 - - + +
77B THR* 4.1 4.3 - - - -
90B MET* 3.8 31.0 - - + -
91B ALA* 1.3 79.5 - - - +
93B GLY* 1.3 64.9 + - - +
144B ILE* 3.5 5.9 - - - +
145B ALA* 2.7 38.2 + - + +
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Residues in contact with GLY 93 (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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100A PHE* 3.4 8.8 - - - -
371A 4CA 3.1 38.9 + - - +
73B GLU* 3.9 16.6 - - - -
77B THR* 4.1 5.5 + - - -
92B VAL* 1.3 75.3 - - - +
94B GLN* 1.3 59.8 + - - -
95B SER 3.7 0.7 - - - -
142B MET* 4.8 2.7 - - - -
143B SER 3.8 6.3 - - - -
144B ILE* 4.1 11.7 - - - -
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Residues in contact with GLN 94 (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 SER* 3.4 5.2 - - - -
100A PHE* 2.9 36.4 + - - +
371A 4CA 3.6 41.3 + - + +
92B VAL 3.3 1.0 + - - -
93B GLY* 1.3 72.6 - - - -
95B SER* 1.3 63.4 + - - +
122B THR* 4.7 10.1 + - - +
143B SER* 2.8 19.3 + - - +
144B ILE 5.2 0.2 - - - -
145B ALA* 3.8 21.0 - - + +
147B ARG* 4.3 9.8 + - - +
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Residues in contact with SER 95 (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 HIS* 2.8 30.7 + - - -
98A THR 3.4 6.5 - - - -
99A SER* 4.4 4.0 - - - -
100A PHE* 4.4 2.2 - - - -
93B GLY 3.7 0.4 - - - -
94B GLN* 1.3 82.5 - - - +
96B ASN* 1.3 61.5 + - - +
97B HIS* 4.1 2.3 + - - +
141B SER 3.6 3.0 + - - +
142B MET* 3.7 5.3 - - - +
143B SER* 2.9 44.1 + - - +
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Residues in contact with ASN 96 (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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69A CYS* 3.9 14.9 - - - -
96A ASN* 3.5 4.0 - - - +
97A HIS* 4.1 1.1 - - - -
98A THR* 2.8 37.3 + - - +
100A PHE* 3.9 9.0 - - + -
69B CYS* 3.0 31.9 + - - -
73B GLU* 3.0 27.6 + - - +
95B SER* 1.3 74.5 + - - +
97B HIS* 1.3 58.5 + - - +
98B THR* 2.8 24.5 + - - -
140B SER* 3.1 6.3 + - - -
141B SER 3.8 2.9 - - - -
142B MET* 3.3 15.4 - - - -
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Residues in contact with HIS 97 (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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95A SER* 2.8 29.2 + - - -
96A ASN 3.5 7.2 - - - -
97A HIS* 3.8 31.8 + + + +
95B SER* 4.1 1.5 - - - +
96B ASN* 1.3 72.5 + - - +
98B THR* 1.4 66.0 + - - +
99B SER* 3.5 14.9 + - - -
139B VAL* 3.8 1.6 - - - +
140B SER* 3.3 1.9 - - - -
141B SER* 2.9 48.3 + - - +
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Residues in contact with THR 98 (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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95A SER* 3.4 2.6 - - - -
96A ASN 2.8 40.1 + - - -
68B TYR* 4.3 13.0 - - + -
69B CYS* 3.7 27.5 - - - +
96B ASN* 2.8 22.7 + - - -
97B HIS* 1.4 72.1 - - - +
99B SER* 1.3 61.3 + - - +
100B PHE* 3.7 29.9 - - + -
129B LEU* 5.1 0.4 - - + -
138B ALA* 4.4 2.2 - - + -
139B VAL 3.2 16.8 - - - +
140B SER* 3.3 11.7 + - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN 3.4 10.1 - - - -
95A SER* 4.2 3.7 + - - -
97B HIS* 3.5 22.3 + - - -
98B THR* 1.3 74.3 - - - +
100B PHE* 1.3 60.5 + - - +
101B PHE* 4.1 14.7 + - - -
138B ALA* 3.2 6.6 - - - +
139B VAL* 2.9 47.0 + - - +
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Residues in contact with PHE 100 (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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73A GLU* 3.6 28.5 - - - -
93A GLY 3.4 26.0 - - - +
94A GLN* 3.0 23.8 + - - +
95A SER 4.5 0.9 - - - -
96A ASN* 4.0 8.3 - - + -
370A 4CA 3.3 40.3 + - + +
65B GLY* 3.5 33.7 - - - -
68B TYR* 3.6 19.5 - + - -
69B CYS* 4.1 4.9 - - - -
98B THR* 3.7 33.7 - - + -
99B SER* 1.3 73.2 - - - +
101B PHE* 1.3 65.6 + - - +
102B ARG 5.7 0.2 - - - +
137B CYS 3.8 3.8 - - - +
138B ALA* 4.1 9.4 - - + -
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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