Contacts of the strand formed by residues 87 - 92 (chain 2) in PDB entry 4C2M
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 SER 87 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102 ILE* 4.3 1.1 - - - -
112 GLU* 3.1 14.4 - - - -
132 GLU* 3.9 25.3 + - - +
812 PHE* 3.4 9.0 - - - -
822 ASN* 3.1 31.1 + - - +
852 LYS* 3.2 35.9 + - - +
862 LYS* 1.3 77.9 - - - +
882 ILE* 1.3 61.5 + - - +
892 GLN* 5.9 1.1 - - - -
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Residues in contact with ILE 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102 ILE* 3.6 21.1 - - + -
112 GLU 2.9 10.6 + - - +
122 ILE* 3.6 11.9 - - + +
132 GLU* 3.0 22.8 + - - -
792 GLY* 4.3 7.9 - - - -
802 LEU 3.2 20.2 - - - +
812 PHE* 4.2 4.9 - - + -
872 SER* 1.3 76.6 - - - +
892 GLN* 1.3 67.3 + - - +
902 LEU* 3.7 29.2 + - + -
543 TRP* 3.6 38.8 - - + -
563 ILE* 4.4 1.8 - - + -
703 LEU* 4.1 14.1 - - + -
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Residues in contact with GLN 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 GLU* 3.5 27.7 + - + +
142 SER* 3.4 25.4 + - - +
792 GLY* 3.4 1.7 - - - -
802 LEU* 2.7 48.7 + - + +
872 SER* 5.9 0.4 - - - +
882 ILE* 1.3 76.9 - - - +
902 LEU* 1.3 62.7 + - - +
912 TYR* 3.4 31.6 + - + -
393 PRO* 3.9 19.5 - - - +
513 GLN* 5.4 2.4 - - - +
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Residues in contact with LEU 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122 ILE* 4.0 26.9 - - + -
142 SER 3.0 7.0 + - - +
152 VAL* 3.2 31.0 - - + -
162 GLN 2.9 24.0 + - - -
772 VAL* 3.9 20.6 - - + -
782 VAL 3.5 2.7 - - - -
792 GLY* 4.2 6.5 - - - -
882 ILE* 3.7 36.3 - - + -
892 GLN* 1.3 73.5 - - - +
912 TYR* 1.3 65.0 + - - +
563 ILE* 4.4 7.9 - - + -
583 PHE* 5.0 6.3 - - + -
643 ILE* 4.2 17.0 - - + -
673 LEU* 4.8 3.1 - - + -
703 LEU* 4.9 3.8 - - + -
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Residues in contact with TYR 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142 SER* 4.4 6.3 + - - -
162 GLN* 3.4 30.3 - - + -
202 SER* 3.6 17.7 - - - +
212 VAL* 4.8 4.3 - - + -
772 VAL* 3.3 5.8 - - - -
782 VAL* 2.8 39.4 + - - +
802 LEU* 3.6 18.4 - - + -
892 GLN* 3.4 40.9 + - + -
902 LEU* 1.3 74.3 - - - +
922 LYS* 1.3 61.2 + - - +
373 ASN 3.4 22.7 - - - -
383 PHE* 3.8 23.8 - + + -
393 PRO* 3.1 31.0 - - + +
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Residues in contact with LYS 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152 VAL* 5.4 3.8 - - + -
162 GLN* 3.3 19.1 + - - +
172 ASP* 3.2 44.2 + - - +
182 GLN 4.3 6.6 - - - +
192 PRO* 5.1 1.7 - - - +
202 SER* 3.6 17.2 + - - -
212 VAL 3.9 3.6 - - - +
492 ASP* 5.7 3.0 + - - -
752 GLN* 3.3 35.3 - - + +
762 TYR 4.3 1.3 - - - +
772 VAL* 3.7 18.4 - - + -
912 TYR* 1.3 73.2 - - - +
932 ALA* 1.3 60.9 + - - +
942 PRO* 4.7 0.7 - - - +
643 ILE* 4.1 11.2 - - + -
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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