Contacts of the helix formed by residues 2114 - 2130 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934H GLU* 5.4 8.0 - - - +
2112H VAL* 3.1 28.3 - - - +
2113H GLN* 1.3 80.8 - - - +
2115H PRO* 1.3 70.5 - - - +
2116H GLU* 3.9 3.5 + - - +
2117H LEU* 3.3 27.9 + - - +
2118H VAL* 3.3 10.3 + - - +
3703H ARG* 6.3 0.4 - - - -
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Residues in contact with PRO2115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2113H GLN 4.7 1.6 - - - +
2114H SER* 1.3 83.6 - - - +
2116H GLU* 1.3 63.7 + - + +
2118H VAL* 3.2 9.5 - - + +
2119H ARG* 2.9 33.7 + - - +
3700H HIS* 3.3 14.7 - - + +
3703H ARG* 4.9 25.3 - - + +
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Residues in contact with GLU2116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938H LEU* 4.9 13.6 - - + +
2114H SER* 3.5 3.7 + - - +
2115H PRO* 1.3 84.1 - - + +
2117H LEU* 1.3 58.0 + - - +
2119H ARG* 3.3 11.6 + - - +
2120H ALA* 2.9 30.3 + - - +
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Residues in contact with LEU2117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934H GLU* 3.2 42.6 - - + +
1937H LYS* 3.6 19.1 - - + -
1938H LEU* 4.0 20.8 - - + +
1941H CYS* 5.1 1.1 - - + -
2112H VAL* 3.5 24.5 - - + -
2114H SER* 3.3 18.0 + - - +
2116H GLU* 1.3 79.9 - - - +
2118H VAL* 1.3 57.4 + - - +
2120H ALA* 3.3 7.3 + - - +
2121H MET* 2.9 57.6 + - + +
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Residues in contact with VAL2118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2112H VAL* 3.9 24.9 - - + -
2114H SER 3.3 15.2 + - - +
2115H PRO* 3.2 13.2 - - + +
2117H LEU* 1.3 78.8 - - - +
2119H ARG* 1.3 62.9 + - - +
2121H MET* 3.3 9.4 + - + +
2122H PHE* 2.9 60.7 + - + -
3696H GLN* 4.8 9.0 - - + +
3700H HIS* 3.5 22.2 - - + +
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Residues in contact with ARG2119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2115H PRO* 2.9 21.2 + - - +
2116H GLU* 3.6 10.0 - - - +
2118H VAL* 1.3 77.8 - - - +
2120H ALA* 1.3 57.1 + - - +
2122H PHE* 3.3 4.3 + - - +
2123H SER* 2.8 31.2 + - - +
3700H HIS* 3.4 25.3 + - - +
3704H THR* 3.4 30.5 - - - +
3715H ASP* 5.9 0.8 - - - +
3717H LEU* 3.5 43.3 - - + +
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Residues in contact with ALA2120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1938H LEU* 5.5 8.7 - - + -
1941H CYS* 3.5 21.2 - - + -
2116H GLU 2.9 18.0 + - - +
2117H LEU* 3.7 6.1 - - - +
2119H ARG* 1.3 77.0 - - - +
2121H MET* 1.3 59.2 + - - +
2123H SER* 2.7 20.0 + - - -
2124H LEU* 2.9 19.9 + - - +
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Residues in contact with MET2121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937H LYS* 6.1 0.4 - - - -
1941H CYS* 4.0 15.5 - - + -
2103H VAL* 3.5 43.6 - - + +
2106H TRP* 3.9 35.2 - - + -
2107H ALA* 4.2 13.2 - - + +
2112H VAL* 5.4 4.5 - - + -
2117H LEU* 2.9 43.6 + - + +
2118H VAL* 3.7 12.8 - - + +
2119H ARG 3.3 0.2 - - - -
2120H ALA* 1.3 76.0 - - - +
2122H PHE* 1.3 64.8 + - + +
2124H LEU* 3.3 3.4 + - - +
2125H LEU* 2.9 29.2 + - - +
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Residues in contact with PHE2122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2107H ALA* 5.5 10.5 - - + -
2118H VAL* 2.9 44.3 + - + +
2119H ARG* 3.8 4.0 - - - +
2121H MET* 1.3 84.2 - - + +
2123H SER* 1.3 57.7 + - - +
2125H LEU* 3.3 9.7 + - + -
2126H HIS 2.9 13.5 + - - -
3673H LEU* 5.3 10.5 - - + -
3693H PRO 4.8 3.6 - - - -
3696H GLN* 4.3 9.9 - - + -
3697H LEU* 3.5 58.6 - - + -
3700H HIS* 4.6 16.6 - + + -
3701H PHE* 6.1 2.9 - + - -
3717H LEU* 5.6 5.2 - - + -
3721H TYR* 2.3 42.0 + + + +
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Residues in contact with SER2123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2119H ARG* 2.8 16.0 + - - +
2120H ALA* 2.7 25.8 + - - -
2122H PHE* 1.3 75.5 - - - +
2124H LEU* 1.3 55.1 + - - +
2126H HIS* 3.3 6.9 + - - +
2127H ARG* 2.9 40.4 + - - +
3716H TYR* 4.8 15.5 - - - -
3717H LEU* 5.3 14.3 - - - +
3721H TYR* 5.2 1.8 - - - -
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Residues in contact with LEU2124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941H CYS* 3.2 44.0 - - - +
1944H LEU* 3.6 28.3 - - + +
1945H GLU* 4.3 14.8 - - + +
1948H CYS* 5.5 6.1 - - + -
2099H VAL* 3.5 28.5 - - + -
2103H VAL* 5.2 7.6 - - + -
2120H ALA 2.9 15.9 + - - +
2121H MET* 3.7 4.3 - - - +
2123H SER* 1.3 76.3 + - - +
2125H LEU* 1.3 57.9 + - - +
2127H ARG* 3.3 8.7 + - + +
2128H GLN* 2.9 30.5 + - + +
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Residues in contact with LEU2125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2099H VAL* 6.0 0.7 - - - -
2100H SER* 5.1 8.1 - - - +
2103H VAL* 3.7 31.8 - - + +
2104H VAL* 4.5 7.0 - - + -
2121H MET 2.9 17.6 + - - +
2122H PHE* 3.6 11.0 - - + +
2124H LEU* 1.3 78.7 - - - +
2126H HIS* 1.3 56.5 + - - +
2128H GLN* 4.1 3.5 - - - +
2129H TYR* 2.9 45.0 + - + +
3669H MET* 6.0 3.6 - - + +
3673H LEU* 4.4 29.6 - - + -
3721H TYR* 3.3 28.7 - - + +
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Residues in contact with HIS2126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2122H PHE 2.9 10.8 + - - +
2123H SER* 3.7 6.7 - - - +
2125H LEU* 1.3 77.7 - - - +
2127H ARG* 1.3 68.6 + - + +
2129H TYR* 5.1 1.8 - - - -
2130H ASP* 3.1 43.7 + - + +
3665H PHE* 4.9 2.1 - + - -
3716H TYR* 6.2 4.7 - + - -
3717H LEU* 6.2 0.9 - - - -
3720H ALA* 3.4 28.8 - - + +
3721H TYR* 3.3 30.5 + + + +
3724H ILE* 3.7 31.0 - - + +
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Residues in contact with ARG2127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734H TYR* 5.8 0.8 + - - -
1945H GLU* 5.2 7.9 + - - +
1948H CYS* 3.9 30.0 - - - +
1949H ASP* 2.5 36.1 + - - +
1952H LEU* 4.3 18.7 - - - +
2123H SER* 2.9 26.4 + - - +
2124H LEU* 3.3 8.9 + - + +
2126H HIS* 1.3 82.6 - - + +
2128H GLN* 1.3 59.6 + - - +
2130H ASP 3.1 19.2 - - - +
2131H GLY* 4.7 2.1 - - - -
2134H GLU* 5.1 10.7 - - - +
3716H TYR* 5.9 4.0 - - + -
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Residues in contact with GLN2128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1948H CYS* 5.2 7.2 - - + -
2043H CYS 5.6 1.6 - - - +
2095H LEU* 6.2 2.0 - - + -
2096H GLN* 4.0 33.3 - - + +
2099H VAL* 4.6 11.2 - - + -
2100H SER* 5.7 2.9 - - - +
2124H LEU* 2.9 28.3 + - + +
2125H LEU* 4.1 4.0 - - - +
2127H ARG* 1.3 77.1 - - - +
2129H TYR* 1.3 62.8 + - - +
2130H ASP 3.5 2.4 + - - -
2131H GLY* 4.7 1.6 + - - -
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Residues in contact with TYR2129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2096H GLN* 5.9 0.4 - - - -
2100H SER* 5.7 10.8 - - - -
2125H LEU* 2.9 27.0 + - + +
2126H HIS* 4.7 1.6 - - - +
2128H GLN* 1.3 76.9 - - - +
2130H ASP* 1.3 58.7 + - + +
2131H GLY 4.0 1.3 + - - -
3665H PHE* 3.5 44.5 + + + +
3668H ARG* 3.4 30.4 + - - +
3669H MET* 3.6 25.1 - - + -
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Residues in contact with ASP2130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2126H HIS* 3.1 30.6 + - + +
2127H ARG* 3.1 17.4 - - - +
2128H GLN 4.6 0.2 - - - -
2129H TYR* 1.3 78.2 - - - +
2131H GLY* 1.3 61.3 + - - +
2132H LEU 3.7 0.9 - - - +
2133H GLY* 4.7 7.9 - - - +
2134H GLU* 3.9 11.4 + - - +
3665H PHE* 3.5 33.7 - - + -
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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