Contacts of the strand formed by residues 92 - 97 (chain M) in PDB entry 3J7Y
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 GLN 92 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1683 ARG* 3.2 15.9 + - - +
1693 ARG 3.9 0.9 - - - +
1703 ASN* 3.1 29.3 + - - +
1713 TRP* 3.2 37.3 + - + +
1723 TYR* 4.2 12.8 - - + +
87M HIS 5.5 0.4 + - - -
90M ARG 4.4 1.8 - - - +
91M ARG* 1.3 74.6 - - - +
93M TYR* 1.3 62.3 + - - +
94M LYS* 4.6 2.6 + - - -
133M LYS 3.2 21.0 + - - -
134M ARG* 3.2 31.6 + - - +
135M ASP* 3.2 12.5 - - - +
136M TYR 2.8 25.9 + - - +
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Residues in contact with TYR 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1713 TRP* 2.9 23.1 + - - +
1733 VAL* 3.2 32.3 - - + -
91M ARG* 3.5 26.7 - - + -
92M GLN* 1.3 74.0 - - - +
94M LYS* 1.3 62.6 + - - +
95M PRO 3.5 1.0 - - - -
136M TYR* 3.2 45.5 - - + +
137M GLY 3.5 8.7 - - - +
138M VAL 4.1 8.3 - - - -
139M GLN* 3.2 35.8 + - + +
157M GLN* 3.9 9.9 - - + -
158M LEU* 3.5 31.8 - - + +
178M PHE* 5.2 1.8 - + - -
210M LEU* 4.1 14.4 - - + +
214M TYR* 4.3 6.4 + - - -
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Residues in contact with LYS 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1683 ARG* 4.2 16.6 - - - +
1693 ARG* 4.5 8.5 + - - +
1713 TRP* 3.8 27.3 - - + +
3806 TYR* 4.9 5.8 - - + -
1891A A 4.0 29.6 + - - +
92M GLN* 4.6 2.4 + - - -
93M TYR* 1.3 70.0 - - - +
95M PRO* 1.3 67.6 - - + +
127M VAL* 4.2 7.7 - - + +
128M THR 3.9 10.5 - - - +
129M ILE* 3.7 27.6 - - + -
130M GLN* 5.1 10.4 - - - +
135M ASP* 3.2 35.0 + - - +
137M GLY 3.1 6.7 + - - -
138M VAL* 3.2 7.4 - - - +
139M GLN 2.8 23.1 + - - -
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Residues in contact with PRO 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1713 TRP* 3.4 42.0 - - + +
3776 TYR* 3.5 24.2 - - + -
3806 TYR* 3.2 38.0 - - + +
93M TYR 3.5 1.5 - - - +
94M LYS* 1.3 85.5 - - + +
96M LEU* 1.3 59.6 + - - +
97M SER 4.0 1.1 - - - +
127M VAL* 4.8 4.3 - - - +
138M VAL* 4.7 0.2 - - - -
139M GLN* 3.4 13.0 - - + +
141M VAL* 3.4 20.2 - - + -
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Residues in contact with LEU 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3806 TYR 4.1 3.8 - - - +
94M LYS 3.8 0.2 + - - -
95M PRO* 1.3 72.5 - - - +
97M SER* 1.3 91.3 + - - +
98M LEU* 3.9 0.4 + - - -
100M ARG* 3.9 10.3 - - + -
101M LEU* 3.7 34.3 - - + +
104M LEU* 5.2 1.3 - - + -
121M LEU* 3.4 41.3 - - + -
127M VAL* 3.6 15.9 - - + -
138M VAL* 3.4 20.2 - - + -
139M GLN 2.7 8.8 + - - +
140M LEU* 3.4 13.1 - - + +
141M VAL* 2.8 26.0 + - - -
154M ILE* 5.9 1.3 - - + -
156M VAL* 5.0 2.2 - - + -
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Residues in contact with SER 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3776 TYR* 5.2 8.8 + - - -
3796 ILE* 5.5 2.6 - - - +
3806 TYR 4.4 10.5 + - - -
95M PRO* 4.0 2.0 + - - +
96M LEU* 1.3 88.8 - - - +
98M LEU* 1.3 66.5 + - - +
99M ASN* 4.2 6.0 - - - +
100M ARG* 2.9 30.7 + - - +
140M LEU* 5.5 0.2 - - - -
141M VAL* 3.8 12.3 - - - +
143M GLU* 3.4 30.7 - - - -
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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