Contacts of the strand formed by residues 2139 - 2146 (chain A) 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 VAL2139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2103A THR* 3.5 19.1 - - - +
2105A ILE* 6.5 0.4 - - + -
2132A SER* 4.4 9.5 - - - -
2133A PRO* 4.5 4.9 - - + +
2136A ASN* 3.6 20.8 + - + +
2137A PRO 4.1 3.6 - - - +
2138A GLN* 1.3 80.8 - - + +
2140A LYS* 1.3 61.9 + - - +
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Residues in contact with LYS2140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2102A TYR* 5.7 5.4 - - + -
2103A THR 2.9 13.0 + - - +
2104A TYR* 3.4 7.1 - - + -
2105A ILE* 2.9 25.7 + - - +
2130A GLY 6.1 0.9 - - - -
2131A VAL 3.7 10.1 - - - +
2132A SER* 4.9 1.8 - - - +
2133A PRO 6.1 0.2 - - - -
2137A PRO 6.0 0.4 - - - +
2138A GLN 3.7 2.8 + - - +
2139A VAL* 1.3 76.5 - - - +
2141A GLU* 1.3 61.9 + - - +
2142A ILE 4.1 0.4 - - - +
2175A LEU* 5.4 12.1 - - + -
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Residues in contact with GLU2141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2105A ILE* 3.5 17.0 - - + +
2130A GLY* 3.0 3.5 - - - -
2131A VAL* 2.9 40.7 + - + +
2132A SER* 5.0 0.4 - - - +
2133A PRO* 5.7 5.6 - - + -
2140A LYS* 1.3 76.0 - - - +
2142A ILE* 1.3 61.6 + - - +
2143A ARG* 3.4 5.5 + - + +
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Residues in contact with ILE2142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104A TYR* 5.4 7.5 - - + +
2105A ILE 2.9 19.7 + - - +
2106A LEU* 4.3 13.6 - - + +
2107A PRO* 4.5 6.2 - - - +
2128A LEU* 4.9 15.5 - - + -
2129A TYR 3.5 14.8 - - - +
2130A GLY* 3.8 2.7 - - - -
2140A LYS* 4.1 1.4 - - - +
2141A GLU* 1.3 71.5 - - - +
2143A ARG* 1.3 59.1 + - - +
2144A CYS 3.6 3.1 - - - +
2175A LEU* 5.4 7.9 - - + -
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Residues in contact with ARG2143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2129A TYR 2.9 7.5 + - - +
2130A GLY* 4.8 3.6 - - - -
2131A VAL* 5.4 2.2 - - + +
2141A GLU* 3.4 9.4 + - + +
2142A ILE* 1.3 73.5 - - - +
2144A CYS* 1.3 62.4 + - - +
2268A LEU 5.4 2.9 - - - +
2269A GLY* 3.5 14.2 - - - -
2270A PHE* 3.3 21.3 + - - +
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Residues in contact with CYS2144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2127A TYR 3.6 0.7 - - - +
2128A LEU* 3.6 5.0 - - - +
2129A TYR* 3.1 41.3 + - + +
2142A ILE* 3.6 3.2 - - - +
2143A ARG* 1.3 81.5 - - - +
2145A ILE* 1.3 60.9 + - - +
2146A VAL* 3.9 2.5 + - + +
2270A PHE* 3.4 12.3 - - + +
2271A PHE* 5.3 4.0 - - - +
2272A MET* 5.8 1.8 - - + +
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Residues in contact with ILE2145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2110A VAL* 5.0 16.0 - - + +
2114A PHE* 5.8 7.0 - - + -
2126A GLY* 5.8 3.4 - - - -
2127A TYR 3.3 7.2 - - - +
2128A LEU* 5.0 0.7 - - - +
2144A CYS* 1.3 71.4 - - - +
2146A VAL* 1.3 60.5 + - - +
2147A MET* 3.8 1.2 + - - +
2270A PHE 3.3 9.0 + - - +
2271A PHE* 3.4 11.6 - - + +
2272A MET 3.4 18.2 + - - -
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Residues in contact with VAL2146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126A GLY* 3.4 6.1 - - - -
2127A TYR* 2.8 54.4 + - + +
2129A TYR* 6.3 2.2 - - + -
2144A CYS* 3.9 3.5 + - + +
2145A ILE* 1.3 71.0 - - - +
2147A MET* 1.3 62.6 + - - +
2148A VAL* 3.7 4.9 + - + +
2164A PRO* 5.4 11.4 - - + -
2272A MET* 4.1 21.5 - - + -
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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