Contacts of the strand formed by residues 2118 - 2124 (chain r) in PDB entry 6FF7
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 GLN2118 (chain r).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2106r LEU 3.7 0.7 - - - +
2107r TYR* 3.3 5.5 - - - +
2108r PHE* 2.9 49.1 + - + +
2116r CYS 3.4 6.6 + - - +
2117r ASP* 1.3 74.1 - - - +
2119r GLU* 1.3 61.6 + - - +
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Residues in contact with GLU2119 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2105r THR* 5.9 3.8 - - - -
2106r LEU 3.3 7.0 - - - +
2107r TYR* 4.7 2.0 - - + +
2117r ASP 4.3 0.6 + - - -
2118r GLN* 1.3 75.6 - - - +
2120r TYR* 1.3 63.5 + - - +
2121r LYS 5.5 0.4 - - - +
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Residues in contact with TYR2120 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2021r TYR* 6.3 2.5 - - + -
2105r THR* 4.5 1.8 - - - -
2106r LEU* 2.9 48.1 + - + +
2119r GLU* 1.3 75.6 - - - +
2121r LYS* 1.3 62.5 + - - +
2122r PHE* 3.6 5.1 + - + +
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Residues in contact with LYS2121 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104r TYR 3.5 10.5 - - - +
2105r THR* 4.3 7.2 - - - +
2119r GLU* 4.3 0.8 - - - +
2120r TYR* 1.3 70.9 - - - +
2122r PHE* 1.3 60.5 + - - +
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Residues in contact with PHE2122 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2103r ASN* 3.2 7.0 - - - +
2104r TYR* 2.9 35.8 + - + +
2106r LEU* 5.9 3.4 - - + +
2120r TYR* 3.6 7.1 + - + +
2121r LYS* 1.3 75.5 - - - +
2123r SER* 1.3 64.7 + - - +
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Residues in contact with SER2123 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2026r LYS* 5.8 1.7 - - - +
2102r HIS 3.8 5.6 - - - -
2103r ASN* 4.1 11.7 - - - -
2122r PHE* 1.3 78.7 - - - +
2124r VAL* 1.3 61.3 + - - +
2125r ASP 4.1 4.7 + - - +
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Residues in contact with VAL2124 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2023r VAL* 5.5 9.4 - - + -
2026r LYS* 4.8 5.6 - - + +
2029r ILE* 6.2 0.7 - - - -
2100r GLY 3.3 9.1 - - - +
2101r ALA* 4.3 0.2 - - - -
2102r HIS* 3.1 27.8 + - + +
2103r ASN* 4.7 0.9 - - - +
2122r PHE 4.4 0.2 + - - -
2123r SER* 1.3 72.7 - - - +
2125r ASP* 1.3 68.5 + - - +
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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