Contacts of the strand formed by residues 78 - 83 (chain 2) in PDB entry 6Q8W
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 TYR 78 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762 GLY 4.2 2.0 - - - -
772 LYS* 1.3 100.3 - - + +
792 HIS* 1.3 60.0 + - - +
802 LEU* 3.5 11.6 + - + +
1162 LEU* 2.7 62.2 + - + +
1172 PHE* 3.6 15.1 - + + -
1182 SER 3.2 15.1 + - - +
1362 VAL* 3.9 23.1 - - + -
1372 ASN* 3.3 3.6 - - - +
1572 LEU* 4.2 38.5 + - + +
1602 GLY* 5.0 8.3 - - - -
1612 LYS 5.1 2.9 + - - -
1632 LEU* 6.3 0.4 - - + -
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Residues in contact with HIS 79 (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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712 GLN* 3.7 22.6 + - + -
752 THR* 2.8 34.3 + - + +
772 LYS 3.9 0.2 - - - -
782 TYR* 1.3 67.4 - - - +
802 LEU* 1.3 63.4 + - - +
812 GLN* 3.2 32.7 + - + +
1082 PRO 5.0 3.4 - - - -
1182 SER* 3.1 12.7 - - - -
1192 VAL 3.8 22.9 - - - -
1202 GLN* 3.2 31.6 + - + +
1352 GLN 3.4 4.2 - - - +
1372 ASN* 2.4 39.0 + - + +
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Residues in contact with LEU 80 (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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782 TYR* 3.8 20.9 - - + +
792 HIS* 1.3 70.4 - - - +
812 GLN* 1.3 60.6 + - - +
822 VAL* 3.8 5.6 + - + +
1002 LEU* 4.4 34.3 - - + -
1042 LEU* 4.6 6.7 - - + -
1172 PHE* 4.0 24.0 - - + -
1182 SER 2.9 19.4 + - - +
1192 VAL* 3.6 4.5 - - + -
1202 GLN* 3.2 26.0 + - - +
1342 ILE* 5.0 12.3 - - + -
1352 GLN 3.8 3.6 - - - -
1362 VAL* 4.2 20.6 - - + -
1532 LEU* 5.2 6.3 - - + -
1542 LEU* 4.7 6.1 - - + -
1572 LEU* 4.8 8.3 - - + -
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Residues in contact with GLN 81 (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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1371 GLU* 5.3 2.9 - - - +
692 TYR* 4.5 18.1 - - - -
792 HIS* 3.4 29.3 + - + +
802 LEU* 1.3 72.1 - - - +
822 VAL* 1.3 61.5 + - - +
832 CYS 3.9 0.5 + - - -
1202 GLN* 3.6 13.0 + - - +
1222 VAL* 3.9 26.4 - - + +
1252 LEU* 4.3 5.6 - - + +
1342 ILE* 3.3 6.8 - - - +
1352 GLN* 2.9 66.0 + - + +
1372 ASN* 3.6 31.5 + - - +
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Residues in contact with VAL 82 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
802 LEU 4.3 7.6 - - - +
812 GLN* 1.3 74.6 - - - +
832 CYS* 1.3 72.7 + - - +
842 ALA* 3.5 1.4 + - + -
932 ALA* 5.0 3.6 - - + +
962 LEU* 4.2 24.7 - - + -
972 TRP* 4.0 36.1 - - + -
1002 LEU* 4.4 13.5 - - + -
1202 GLN 3.0 12.0 + - - +
1212 LYS* 3.5 6.7 - - + +
1222 VAL* 2.6 34.8 + - - +
1332 VAL 4.2 3.6 - - - +
1342 ILE* 4.2 18.4 - - + -
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Residues in contact with CYS 83 (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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812 GLN 3.9 1.8 + - - -
822 VAL* 1.3 83.2 - - - +
842 ALA* 1.3 61.9 - - - +
852 THR* 3.6 22.2 - - - -
882 CYS* 3.8 26.2 - - - +
932 ALA* 3.6 14.6 - - - +
962 LEU* 5.9 0.2 - - - +
1222 VAL 3.2 6.1 - - - -
1232 GLU 3.7 9.9 - - - -
1242 CYS* 3.9 2.7 - - - -
1252 LEU* 3.8 29.2 - - + +
1322 PRO* 5.7 1.0 - - - +
1332 VAL* 3.4 25.8 + - + +
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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