Contacts of the helix formed by residues 2114 - 2130 (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 SER2114 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934F GLU* 5.4 7.7 - - - +
2112F VAL* 3.1 28.3 - - - +
2113F GLN* 1.3 81.3 - - - +
2115F PRO* 1.3 69.9 - - - +
2116F GLU* 3.9 3.3 + - - +
2117F LEU* 3.3 27.0 + - - +
2118F VAL* 3.3 10.7 + - - +
3703F ARG* 6.3 0.2 - - - -
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Residues in contact with PRO2115 (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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2113F GLN 4.7 1.6 - - - +
2114F SER* 1.3 83.5 - - - +
2116F GLU* 1.3 62.7 + - + +
2118F VAL* 3.2 9.7 - - + +
2119F ARG* 2.9 34.7 + - - +
3700F HIS* 3.3 14.1 - - + +
3703F ARG* 4.9 26.4 - - + +
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Residues in contact with GLU2116 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938F LEU* 4.9 13.6 - - + +
2114F SER* 3.5 3.1 + - - +
2115F PRO* 1.3 83.0 - - + +
2117F LEU* 1.3 58.5 + - - +
2119F ARG* 3.3 12.1 + - - +
2120F ALA* 2.9 30.4 + - - +
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Residues in contact with LEU2117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934F GLU* 3.2 42.8 - - + +
1937F LYS* 3.6 20.2 - - + -
1938F LEU* 4.0 18.5 - - + +
1941F CYS* 5.1 1.0 - - + -
2112F VAL* 3.5 25.4 - - + -
2114F SER* 3.3 18.8 + - - +
2116F GLU* 1.3 78.5 - - - +
2118F VAL* 1.3 57.3 + - - +
2120F ALA* 3.3 6.5 + - - +
2121F MET* 2.9 58.0 + - + +
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Residues in contact with VAL2118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2112F VAL* 3.9 25.6 - - + -
2114F SER 3.3 13.1 + - - +
2115F PRO* 3.2 13.5 - - + +
2117F LEU* 1.3 80.0 - - - +
2119F ARG* 1.3 62.5 + - - +
2121F MET* 4.3 9.0 - - + -
2122F PHE* 2.9 60.6 + - + -
3696F GLN* 4.8 9.4 - - + +
3700F HIS* 3.5 22.9 - - + +
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Residues in contact with ARG2119 (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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2115F PRO* 2.9 21.0 + - - +
2116F GLU* 3.6 9.8 - - - +
2118F VAL* 1.3 77.8 - - - +
2120F ALA* 1.3 57.5 + - - +
2122F PHE* 3.3 4.2 + - - +
2123F SER* 2.8 31.8 + - - +
3700F HIS* 3.4 25.1 + - - +
3704F THR* 3.4 30.5 - - - +
3715F ASP* 5.9 0.8 - - - +
3717F LEU* 3.5 43.7 - - + +
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Residues in contact with ALA2120 (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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1938F LEU* 5.5 8.7 - - + -
1941F CYS* 3.5 21.5 - - + -
2116F GLU 2.9 16.9 + - - +
2117F LEU* 3.7 6.3 - - - +
2119F ARG* 1.3 77.1 - - - +
2121F MET* 1.3 58.3 + - - +
2123F SER* 2.7 19.7 + - - -
2124F LEU* 2.9 20.4 + - - +
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Residues in contact with MET2121 (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* 6.1 0.4 - - - +
1941F CYS* 4.0 14.6 - - + -
2103F VAL* 3.5 44.1 - - + +
2106F TRP* 3.9 36.8 - - + -
2107F ALA* 4.2 13.2 - - + +
2112F VAL* 5.4 4.0 - - + -
2117F LEU* 2.9 44.0 + - + +
2118F VAL* 3.7 13.0 - - + +
2120F ALA* 1.3 76.0 - - - +
2122F PHE* 1.3 63.8 + - + +
2124F LEU* 3.3 3.4 + - - +
2125F LEU* 2.9 29.5 + - - +
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Residues in contact with PHE2122 (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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2107F ALA* 5.5 10.8 - - + -
2118F VAL* 2.9 45.3 + - + +
2119F ARG* 3.8 4.7 - - - +
2121F MET* 1.3 81.8 - - + +
2123F SER* 1.3 58.5 + - - +
2125F LEU* 3.3 9.4 + - + -
2126F HIS* 2.9 13.3 + - - +
3673F LEU* 5.3 11.2 - - + -
3693F PRO 4.8 3.6 - - - -
3696F GLN* 4.3 10.1 - - + -
3697F LEU* 3.5 57.9 - - + -
3700F HIS* 4.6 15.9 - + + -
3701F PHE* 6.1 2.9 - + - -
3717F LEU* 5.6 4.9 - - + -
3721F TYR* 2.3 41.7 + + + +
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Residues in contact with SER2123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2119F ARG* 2.8 16.2 + - - +
2120F ALA* 2.7 26.2 + - - -
2122F PHE* 1.3 76.7 - - - +
2124F LEU* 1.3 55.6 + - - +
2126F HIS* 3.3 7.1 + - - +
2127F ARG* 2.9 40.8 + - - +
3716F TYR* 4.8 15.3 - - - -
3717F LEU* 5.3 15.1 - - - +
3721F TYR* 4.9 2.4 - - - -
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Residues in contact with LEU2124 (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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1941F CYS* 3.2 43.1 - - - +
1944F LEU* 3.6 28.5 - - + +
1945F GLU* 4.3 14.1 - - + +
1948F CYS* 5.5 6.3 - - + -
2099F VAL* 3.5 28.7 - - + -
2103F VAL* 5.2 7.0 - - + -
2120F ALA 2.9 16.5 + - - +
2121F MET* 3.7 4.5 - - - +
2123F SER* 1.3 76.9 + - - +
2125F LEU* 1.3 59.9 + - - +
2127F ARG* 3.3 8.9 + - + +
2128F GLN* 2.9 31.0 + - + +
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Residues in contact with LEU2125 (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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2099F VAL* 6.0 0.9 - - - -
2100F SER* 5.2 7.2 - - - +
2103F VAL* 3.7 31.5 - - + +
2104F VAL* 4.5 7.4 - - + -
2121F MET 2.9 16.9 + - - +
2122F PHE* 3.3 10.7 + - + +
2124F LEU* 1.3 77.0 - - - +
2126F HIS* 1.3 57.3 + - - +
2128F GLN* 4.0 3.5 - - - +
2129F TYR* 2.9 44.3 + - + +
3669F MET* 6.0 3.8 - - + +
3673F LEU* 4.4 29.6 - - + -
3721F TYR* 3.3 29.2 - - + +
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Residues in contact with HIS2126 (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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2122F PHE 2.9 10.8 + - - +
2123F SER* 3.7 6.1 - - - +
2125F LEU* 1.3 78.3 - - - +
2127F ARG* 1.3 68.8 + - + +
2129F TYR* 5.1 2.0 - - - -
2130F ASP* 3.1 44.5 + - + +
3665F PHE* 4.9 1.9 - + - -
3716F TYR* 6.2 4.5 - + - -
3717F LEU* 6.2 0.9 - - - -
3720F ALA* 3.4 29.8 - - + +
3721F TYR* 3.3 30.0 + + + +
3724F ILE* 3.7 31.6 - - + +
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Residues in contact with ARG2127 (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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1734F TYR* 5.8 0.8 + - - -
1945F GLU* 5.2 8.4 + - - +
1948F CYS* 3.9 31.2 - - - +
1949F ASP* 2.5 36.5 + - - +
1952F LEU* 4.3 19.0 - - - +
2123F SER* 2.9 26.2 + - - +
2124F LEU* 3.8 7.4 - - + +
2126F HIS* 1.3 83.8 - - + +
2128F GLN* 1.3 59.9 + - - +
2130F ASP 3.1 18.6 - - - +
2131F GLY* 4.7 2.6 - - - -
2134F GLU* 5.1 10.0 - - - +
3716F TYR* 5.9 4.3 - - + -
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Residues in contact with GLN2128 (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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1948F CYS* 5.0 6.9 - - + -
2043F CYS 5.6 1.2 - - - +
2095F LEU* 6.2 2.2 - - + -
2096F GLN* 4.0 33.4 - - + +
2099F VAL* 4.6 11.7 - - + -
2100F SER* 5.7 3.1 - - - +
2124F LEU* 2.9 28.5 + - + +
2125F LEU* 4.0 3.6 - - - +
2127F ARG* 1.3 78.7 - - - +
2129F TYR* 1.3 63.0 + - - +
2130F ASP 3.5 2.3 + - - -
2131F GLY* 4.7 1.7 + - - -
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Residues in contact with TYR2129 (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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2096F GLN* 5.9 0.2 - - - -
2100F SER* 5.7 10.5 - - - -
2125F LEU* 2.9 28.2 + - + +
2126F HIS* 4.7 2.2 - - - +
2128F GLN* 1.3 77.1 - - - +
2130F ASP* 1.3 56.3 + - - +
2131F GLY 4.0 1.7 + - - -
3665F PHE* 3.5 45.8 + + + +
3668F ARG* 3.4 30.5 + - - +
3669F MET* 3.6 25.1 - - + -
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Residues in contact with ASP2130 (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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2126F HIS* 3.1 30.7 + - + +
2127F ARG* 3.1 17.4 - - - +
2128F GLN 4.6 0.4 - - - -
2129F TYR* 1.3 76.6 - - - +
2131F GLY* 1.3 59.6 + - - +
2132F LEU 3.7 0.9 - - - +
2133F GLY* 4.7 8.3 - - - +
2134F GLU* 3.9 11.8 + - - +
3665F PHE* 3.5 34.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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