Contacts of the strand formed by residues 117 - 122 (chain 2) in PDB entry 6Q8O
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 PHE 117 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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782 TYR* 3.4 31.6 - + + -
802 LEU* 4.3 17.0 - - + -
1042 LEU* 4.7 15.0 - - + -
1062 ILE* 3.5 8.8 - - + +
1112 VAL* 3.3 2.3 - - - +
1122 THR* 2.5 55.0 + - + +
1142 ASP* 4.8 3.4 - - - -
1152 GLY 3.9 0.4 - - - -
1162 LEU* 1.3 109.9 - - + +
1182 SER* 1.3 61.6 + - - +
1542 LEU* 3.8 39.3 - - + -
1572 LEU* 4.4 8.3 - - + -
1582 ARG* 3.9 26.5 - - + -
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Residues in contact with SER 118 (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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752 THR* 3.3 22.7 + - - -
762 GLY* 2.9 21.3 + - - -
782 TYR 2.9 8.1 + - - +
792 HIS* 3.6 9.0 - - - -
802 LEU* 2.8 35.7 + - - +
1062 ILE* 5.0 1.6 - - - -
1082 PRO 5.2 0.4 - - - -
1092 GLY 5.6 0.7 - - - -
1102 GLU 3.2 23.7 + - - -
1112 VAL* 3.3 10.2 - - - +
1162 LEU 4.3 0.2 - - - -
1172 PHE* 1.3 69.9 - - - +
1192 VAL* 1.3 62.7 + - - +
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Residues in contact with VAL 119 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792 HIS* 4.0 3.3 - - - -
802 LEU* 3.5 7.2 - - + -
972 TRP* 3.7 18.8 - - + -
1002 LEU* 4.2 17.0 - - + -
1012 THR* 5.2 5.8 - - - +
1042 LEU* 3.9 28.0 - - + -
1062 ILE* 3.7 18.2 - - + +
1072 GLY 3.2 32.3 - - - +
1082 PRO* 2.7 29.7 - - + +
1102 GLU 4.3 0.8 + - - -
1182 SER* 1.3 80.1 - - - +
1202 GLN* 1.3 63.0 + - - +
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Residues in contact with GLN 120 (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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682 SER* 3.6 16.7 + - - -
692 TYR* 5.0 2.0 + - - +
712 GLN* 2.2 37.4 + - - +
792 HIS* 2.3 28.2 + - + +
802 LEU 2.8 13.2 + - - +
812 GLN* 3.3 16.0 + - - +
822 VAL* 2.8 25.8 + - - -
972 TRP* 3.8 10.1 - - - -
1082 PRO* 4.7 7.9 - - + +
1192 VAL* 1.3 79.5 - - - +
1212 LYS* 1.3 69.7 + - - +
1222 VAL* 3.6 20.8 - - + +
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Residues in contact with LYS 121 (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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3461 ARG* 4.3 26.5 - - - +
3501 HIS* 5.1 9.8 + - + -
682 SER* 5.5 3.8 - - - -
822 VAL* 3.5 6.5 - - + +
842 ALA* 3.7 30.5 - - + -
942 GLU* 5.8 3.2 + - - +
972 TRP* 4.0 49.2 - - + +
1082 PRO* 5.3 6.6 - - - +
1202 GLN* 1.3 84.4 + - - +
1222 VAL* 1.3 65.4 + - - +
1232 GLU* 5.3 4.0 - - - +
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Residues in contact with VAL 122 (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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1351 ARG* 5.5 1.3 - - - +
1371 GLU* 4.5 10.5 - - - +
3501 HIS* 5.4 3.1 - - - -
682 SER* 5.6 6.7 - - - -
812 GLN* 3.3 40.2 - - + +
822 VAL 2.9 11.8 + - - +
832 CYS* 3.5 0.5 - - - -
842 ALA* 3.2 24.3 + - - +
1202 GLN* 3.6 12.8 - - - +
1212 LYS* 1.3 82.4 - - - +
1232 GLU* 1.3 85.8 + - - +
1242 CYS 5.4 0.2 - - - +
1252 LEU* 3.7 20.0 - - + -
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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