Contacts of the strand formed by residues 122 - 125 (chain 3) in PDB entry 5OOM
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 TRP 122 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1103 VAL* 4.4 7.0 - - + -
1113 ILE* 6.0 2.2 - - + -
1143 PHE* 3.6 31.2 - - + -
1153 LEU 3.3 4.5 - - - -
1163 ARG* 3.6 44.9 - - + +
1203 GLY 3.5 6.6 + - - -
1213 LEU* 1.3 73.5 - - - +
1233 VAL* 1.3 61.2 + - - +
1493 PHE* 3.5 3.0 - - - -
1503 CYS* 3.0 42.0 + - + +
1553 SER* 3.2 38.3 + - - -
1583 LEU* 3.5 49.4 - - + -
1593 ASP* 3.3 24.0 + - - -
1623 THR* 4.0 20.6 - - + -
1663 TRP* 5.7 2.7 - - + -
1673 LYS* 5.1 0.2 - - - -
3576 PHE* 5.8 0.2 - - - -
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Residues in contact with VAL 123 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1143 PHE* 3.5 6.5 - - - -
1153 LEU* 2.8 42.9 + - + +
1173 LEU* 3.8 20.4 - - + -
1223 TRP* 1.3 74.6 - - - +
1243 ARG* 1.3 65.8 + - - +
1473 PHE* 3.8 36.3 - - + -
1483 VAL 3.8 3.1 - - - -
1493 PHE* 3.7 29.8 - - + -
3636 LEU* 3.7 16.8 - - + -
83M PHE* 4.1 13.2 - - + -
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Residues in contact with ARG 124 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133 ARG 4.4 6.1 - - - +
1143 PHE* 3.6 15.9 - - + -
1233 VAL* 1.3 75.2 - - - +
1253 ARG* 1.3 75.9 + - - +
1263 LYS* 3.9 6.7 - - - +
1473 PHE* 3.5 8.5 - - - -
1483 VAL* 2.9 62.0 + - + +
1493 PHE 4.4 1.0 + - - -
1503 CYS* 3.8 17.7 - - - -
1543 GLN* 5.0 0.2 + - - -
3606 ARG* 4.1 2.0 - - - +
2868A C 2.9 41.3 + - - -
2869A A 2.8 32.3 + - - -
74M PHE* 3.9 8.7 - - - -
78M ILE* 3.7 28.7 - - + +
83M PHE* 4.3 7.6 - - - -
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Residues in contact with ARG 125 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1133 ARG 4.7 1.0 + - - +
1243 ARG* 1.3 90.5 + - - +
1263 LYS* 1.3 66.4 + - - +
1293 TYR* 3.5 54.8 - - + +
1443 LEU 4.8 0.7 - - - -
1453 ARG* 4.0 23.6 + - - +
1463 GLU 3.9 7.0 - - - -
1473 PHE* 3.2 34.4 - - + -
78M ILE* 3.4 15.6 - - - +
79M PRO* 4.1 12.3 - - + +
81M TYR* 3.3 51.8 + - + -
83M PHE* 4.6 2.9 - - + -
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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