Contacts of the strand formed by residues 89 - 100 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL* 3.1 32.0 + - + +
85A HIS* 3.7 18.7 - - - -
87A LYS* 3.8 16.6 - - + +
88A GLY* 1.3 83.6 - - - +
90A MET* 1.3 61.8 + - - +
120A SER 4.7 6.1 - - - +
146A VAL* 3.4 27.1 - - + +
147A ARG* 3.0 37.7 - - - +
148A PRO* 3.5 19.7 - - + -
149A ARG* 3.7 9.7 + - - -
372A EDO 4.3 2.1 + - - -
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Residues in contact with MET 90 (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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89A MET* 1.3 74.4 - - - -
91A ALA* 1.3 62.9 + - - +
92A VAL* 3.7 35.9 - - + -
145A ALA 5.3 0.2 - - - +
146A VAL* 3.4 4.7 - - - +
147A ARG* 2.3 55.5 + - + +
148A PRO 4.5 2.7 - - - +
149A ARG* 3.9 14.5 - - + +
370A 4CA 3.0 66.9 - - + +
372A EDO 3.1 15.5 - - - +
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Residues in contact with ALA 91 (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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77A THR* 3.4 11.7 - - - +
80A THR* 3.7 30.7 - - + -
81A VAL* 4.0 16.4 - - + -
84A VAL* 4.1 7.6 - - + +
90A MET* 1.3 75.8 - - - +
92A VAL* 1.3 60.3 + - - +
144A ILE* 3.8 7.9 - - + -
145A ALA 3.2 6.5 - - - +
146A VAL* 4.7 0.9 - - + -
372A EDO 2.7 32.7 + - - -
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Residues in contact with VAL 92 (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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77A THR* 4.1 4.5 - - - -
90A MET* 3.7 23.6 - - + -
91A ALA* 1.3 81.0 - - - +
93A GLY* 1.3 63.4 + - - +
144A ILE* 3.8 4.9 - - - +
145A ALA* 2.8 29.4 + - + +
370A 4CA 3.8 65.5 - - + +
372A EDO 3.4 13.7 - - - +
58B GLN* 5.8 0.2 - - - +
62B LEU* 5.1 9.9 - - + -
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Residues in contact with GLY 93 (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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73A GLU* 4.0 12.3 - - - -
77A THR* 4.1 9.3 + - - -
92A VAL* 1.3 75.6 - - - +
94A GLN* 1.3 61.5 + - - +
95A SER 3.6 0.9 - - - -
142A MET* 4.8 2.9 - - - -
143A SER 3.6 8.1 - - - -
144A ILE* 3.9 13.2 - - - -
370A 4CA 3.4 33.6 + - - +
100B PHE* 3.4 9.5 - - - +
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Residues in contact with GLN 94 (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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92A VAL 3.4 0.8 + - - -
93A GLY* 1.3 76.9 - - - +
95A SER* 1.3 62.3 + - - +
122A THR* 4.2 14.8 + - - -
143A SER* 2.7 20.0 + - - +
145A ALA* 3.7 25.0 - - + +
147A ARG* 4.1 10.7 + - - +
370A 4CA 3.7 36.1 + - + +
99B SER* 3.4 6.1 - - - -
100B PHE* 3.0 32.1 + - - +
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Residues in contact with SER 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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93A GLY 3.6 0.4 - - - -
94A GLN* 1.3 84.2 - - - +
96A ASN* 1.3 61.2 + - - +
97A HIS* 4.2 2.8 + - - +
141A SER 3.7 1.5 + - - +
142A MET* 3.6 6.6 - - - +
143A SER* 2.8 45.2 + - - +
97B HIS* 2.8 31.4 + - - -
98B THR 3.4 5.8 - - - -
99B SER* 4.5 3.8 - - - -
100B PHE* 4.4 1.8 - - - -
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Residues in contact with ASN 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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69A CYS* 2.9 36.1 + - - +
73A GLU* 2.9 28.3 + - - +
95A SER* 1.3 72.5 + - - +
97A HIS* 1.3 59.0 + - - +
98A THR* 2.7 25.8 + - - -
140A SER* 3.3 4.0 + - - -
141A SER 3.7 3.1 - - - -
142A MET* 3.3 15.4 - - - -
69B CYS* 3.9 13.0 - - - -
96B ASN* 3.5 2.4 - - - +
97B HIS* 3.5 2.2 - - - -
98B THR* 2.8 38.3 + - - +
100B PHE* 4.0 9.0 - - + -
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Residues in contact with HIS 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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95A SER* 4.2 1.8 - - - +
96A ASN* 1.3 71.8 + - - +
98A THR* 1.3 66.6 + - - +
99A SER* 3.6 14.9 + - - -
139A VAL* 3.8 1.2 - - - +
140A SER* 3.2 1.4 - - - -
141A SER* 2.7 50.6 + - - +
95B SER* 2.8 28.6 + - - -
96B ASN 3.5 7.2 - - - -
97B HIS* 3.8 31.8 + + + +
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Residues in contact with THR 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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68A TYR* 4.4 8.3 - - + -
69A CYS* 3.7 25.4 - - - +
96A ASN* 2.7 23.9 + - - -
97A HIS* 1.3 72.7 - - - +
99A SER* 1.3 65.1 + - - +
100A PHE* 3.6 30.0 - - + -
129A LEU* 5.1 0.4 - - + -
138A ALA* 4.4 6.1 - - + -
139A VAL 3.2 14.6 - - - +
140A SER* 3.3 12.9 + - - -
95B SER* 3.4 2.1 - - - -
96B ASN 2.8 38.2 + - - -
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Residues in contact with SER 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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97A HIS* 3.6 22.9 + - - -
98A THR* 1.3 74.6 - - - +
100A PHE* 1.3 62.3 + - - +
101A PHE* 4.0 14.5 + - - -
138A ALA* 3.2 6.6 - - - +
139A VAL* 2.9 46.6 + - - +
94B GLN 3.4 8.3 - - - -
95B SER* 4.3 3.5 + - - -
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Residues in contact with PHE 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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65A GLY* 3.5 30.7 - - - -
68A TYR* 3.7 16.4 - + - -
69A CYS* 4.0 5.8 - - - -
98A THR* 3.6 36.3 - - + -
99A SER* 1.3 71.8 - - - +
101A PHE* 1.3 66.9 + - - +
102A ARG 5.8 0.2 - - - +
137A CYS 3.9 2.7 - - - +
138A ALA* 4.1 11.7 - - + -
371A 4CA 3.4 38.4 + - + +
73B GLU* 3.5 28.7 - - - -
93B GLY 3.4 27.4 - - - +
94B GLN* 2.9 26.6 + - - +
95B SER 4.4 1.1 - - - -
96B ASN* 3.9 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