Contacts of the helix formed by residues 2094 - 2110 (chain F) in PDB entry 6X34
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 SER2094 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761F HIS* 5.4 12.3 - - - -
2092F LEU* 3.1 8.2 - - - +
2093F GLN* 1.3 79.3 - - - +
2095F LEU* 1.3 65.3 + - - +
2096F GLN* 4.6 2.0 - - - -
2097F GLU* 3.8 23.0 - - - +
2098F LEU* 3.1 29.0 + - - +
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Residues in contact with LEU2095 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1761F HIS* 6.2 1.2 - - - +
1764F PRO* 3.7 38.4 - - + -
1871F VAL* 6.3 2.9 - - + -
1944F LEU* 5.6 5.4 - - + +
1947F PHE* 4.7 17.3 - - + +
1948F CYS* 5.4 9.9 - - + +
1951F GLU* 4.2 23.3 - - - +
2094F SER* 1.3 71.9 - - - +
2096F GLN* 1.3 61.5 + - + +
2098F LEU* 3.3 14.4 - - + +
2099F VAL* 2.9 49.8 + - + +
2128F GLN* 6.2 2.2 - - + -
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Residues in contact with GLN2096 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2094F SER* 3.4 2.4 - - - -
2095F LEU* 1.3 85.2 - - + +
2097F GLU* 1.3 57.9 + - - +
2099F VAL* 3.4 5.0 + - - +
2100F SER* 2.9 31.6 + - - -
2128F GLN* 4.0 30.3 - - + +
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Residues in contact with GLU2097 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2092F LEU* 3.9 18.6 - - + +
2094F SER* 3.5 23.1 + - - +
2095F LEU 3.3 0.6 - - - -
2096F GLN* 1.3 79.8 - - - +
2098F LEU* 1.3 56.2 + - - +
2100F SER* 2.9 23.4 + - - -
2101F HIS* 2.9 23.9 + - + +
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Residues in contact with LEU2098 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1867F ILE* 6.0 4.9 - - + -
1868F GLU* 5.3 11.0 - - + -
1870F GLU* 5.9 4.3 - - + -
1871F VAL* 4.1 27.1 - - + +
1928F LEU* 6.4 2.2 - - + -
1944F LEU* 5.4 5.2 - - + -
2092F LEU* 4.0 20.6 - - + +
2093F GLN* 5.9 0.7 - - - +
2094F SER 3.1 22.2 + - - +
2095F LEU* 3.3 20.4 - - + +
2097F GLU* 1.3 78.9 - - - +
2099F VAL* 1.3 64.7 + - + +
2101F HIS* 3.3 6.3 + - - +
2102F THR* 2.5 43.6 + - + +
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Residues in contact with VAL2099 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1944F LEU* 3.9 30.5 - - + -
2095F LEU* 2.9 39.2 + - + +
2096F GLN* 3.8 5.8 - - - +
2098F LEU* 1.3 89.0 - - + +
2100F SER* 1.3 58.3 + - - +
2102F THR* 2.9 18.1 + - - -
2103F VAL* 2.9 26.3 + - + +
2124F LEU* 3.5 31.2 - - + -
2125F LEU* 6.0 0.9 - - - +
2128F GLN* 4.6 7.2 - - + -
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Residues in contact with SER2100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2096F GLN 2.9 16.4 + - - -
2097F GLU* 2.9 13.2 + - - -
2099F VAL* 1.3 76.2 - - - +
2101F HIS* 1.3 71.2 + - - +
2103F VAL* 3.0 12.2 - - - +
2104F VAL* 2.9 35.0 + - - +
2125F LEU* 5.2 8.3 - - - +
2128F GLN* 5.7 3.1 - - - +
2129F TYR* 5.7 11.0 - - - -
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Residues in contact with HIS2101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2092F LEU* 3.8 29.8 - - + +
2097F GLU* 2.9 21.4 + - + +
2098F LEU* 3.6 6.1 - - - +
2099F VAL 3.2 0.2 - - - -
2100F SER* 1.3 89.8 + - - +
2102F THR* 1.3 56.6 + - + +
2104F VAL* 3.1 12.1 - - - +
2105F ARG* 2.9 30.9 + - - +
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Residues in contact with THR2102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1928F LEU* 4.1 41.5 - - + +
1929F GLN* 4.6 8.1 - - - +
1944F LEU* 4.9 6.1 - - - +
2098F LEU* 2.5 30.9 + - + +
2099F VAL* 2.9 15.8 + - - +
2101F HIS* 1.3 74.5 - - + +
2103F VAL* 1.3 58.4 + - - +
2105F ARG* 3.3 4.9 + - + +
2106F TRP* 2.9 47.4 + - - +
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Residues in contact with VAL2103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1944F LEU* 5.6 3.4 - - + -
2099F VAL* 2.9 30.4 + - + +
2100F SER* 3.0 26.0 - - - +
2102F THR* 1.3 77.9 - - - +
2104F VAL* 1.3 58.0 + - - +
2106F TRP* 3.3 9.9 + - + -
2107F ALA* 2.9 28.8 + - - +
2121F MET* 3.5 40.8 - - + +
2124F LEU* 5.2 9.6 - - + -
2125F LEU* 3.7 29.8 - - + +
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Residues in contact with VAL2104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2100F SER* 2.9 26.9 + - - +
2101F HIS* 3.1 21.3 - - - +
2103F VAL* 1.3 80.7 - - + +
2105F ARG* 1.3 56.9 + - + +
2107F ALA* 3.7 6.6 - - - +
2108F GLN* 2.9 31.4 + - - +
2125F LEU* 4.5 6.5 - - + -
3672F ASP* 4.6 14.8 - - + +
3673F LEU* 4.1 25.6 - - + -
3693F PRO* 5.2 2.8 - - + +
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Residues in contact with ARG2105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2101F HIS 2.9 19.0 + - - +
2102F THR* 3.7 7.9 - - + +
2103F VAL 3.2 0.2 - - - -
2104F VAL* 1.3 79.1 - - + +
2106F TRP* 1.3 60.5 + - + +
2108F GLN* 3.3 4.5 + - - +
2109F GLU* 2.9 31.5 + - - +
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Residues in contact with TRP2106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1928F LEU* 3.5 40.7 + - + -
1930F MET 5.6 1.6 + - - -
1937F LYS* 3.5 67.0 + - + +
1940F MET* 4.0 24.0 - - + -
1941F CYS* 4.9 6.3 - - + -
1944F LEU* 5.5 7.0 - - + -
2102F THR* 2.9 30.1 + - - +
2103F VAL* 3.7 13.5 - - + +
2105F ARG* 1.3 82.6 - - + +
2107F ALA* 1.3 61.6 - - - +
2108F GLN 3.6 0.2 + - - -
2109F GLU* 3.6 15.2 + - + +
2110F ASP 4.0 7.6 + - - +
2112F VAL* 5.4 2.9 - - - +
2121F MET* 3.9 33.2 - - + -
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Residues in contact with ALA2107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2103F VAL 2.9 17.6 + - - +
2104F VAL* 3.7 7.0 - - - +
2106F TRP* 1.3 78.3 - - - +
2108F GLN* 1.3 59.2 + - - +
2110F ASP 3.5 13.5 - - - +
2112F VAL* 5.6 6.4 - - - +
2121F MET* 4.2 10.0 - - + +
2122F PHE* 5.5 10.1 - - + -
3673F LEU* 5.6 5.2 - - + -
3691F PRO 5.3 2.1 - - - +
3693F PRO* 4.3 21.9 - - + +
3696F GLN* 4.2 20.8 + - - +
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Residues in contact with GLN2108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2104F VAL 2.9 17.7 + - - +
2105F ARG* 4.1 4.4 - - - +
2107F ALA* 1.3 75.7 - - - +
2109F GLU* 1.3 68.0 + - - +
2110F ASP* 4.6 0.6 - - - -
3676F ALA* 3.2 52.3 + - + +
3691F PRO 6.0 0.7 - - - -
3693F PRO* 3.9 11.4 - - + -
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Residues in contact with GLU2109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937F LYS* 6.3 0.7 - - - +
2105F ARG 2.9 17.3 + - - +
2106F TRP* 3.9 10.8 - - + +
2107F ALA 3.4 0.8 - - - -
2108F GLN* 1.3 82.5 - - - +
2110F ASP* 1.3 65.0 + - + +
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Residues in contact with ASP2110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2106F TRP 4.0 7.2 + - - +
2107F ALA 3.5 15.9 - - - +
2108F GLN 3.6 0.4 - - - -
2109F GLU* 1.3 82.2 - - + +
2111F PHE* 1.3 70.9 + - - +
2112F VAL* 3.8 4.0 + - - +
3691F PRO* 6.3 0.4 - - - -
3696F GLN* 5.0 2.2 + - - -
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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