Contacts of the helix formed by residues 2114 - 2130 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934B GLU* 5.4 7.5 - - - +
2112B VAL* 3.1 28.1 - - - +
2113B GLN* 1.3 80.0 - - - +
2115B PRO* 1.3 71.2 - - - +
2116B GLU* 3.9 3.1 + - - +
2117B LEU* 3.3 27.6 + - - +
2118B VAL* 3.3 11.0 + - - +
3703B ARG* 6.3 0.2 - - - -
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Residues in contact with PRO2115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2113B GLN 4.7 1.6 - - - +
2114B SER* 1.3 82.9 - - - +
2116B GLU* 1.3 63.4 + - + +
2118B VAL* 3.2 9.9 - - + +
2119B ARG* 2.9 34.6 + - - +
3700B HIS* 3.3 13.1 - - + +
3703B ARG* 4.9 25.1 - - + +
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Residues in contact with GLU2116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938B LEU* 4.9 13.6 - - + +
2114B SER* 3.5 2.6 + - - +
2115B PRO* 1.3 83.6 - - + +
2117B LEU* 1.3 58.9 + - - +
2119B ARG* 3.3 11.3 + - - +
2120B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU2117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1934B GLU* 3.2 43.1 - - + +
1937B LYS* 3.6 20.6 - - + -
1938B LEU* 4.0 19.4 - - + +
1941B CYS* 5.1 1.2 - - + +
2112B VAL* 3.5 25.1 - - + -
2114B SER* 3.3 18.8 + - - +
2116B GLU* 1.3 79.9 - - - +
2118B VAL* 1.3 56.5 + - - +
2120B ALA* 3.3 5.7 + - - +
2121B MET* 2.9 57.7 + - + +
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Residues in contact with VAL2118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2112B VAL* 3.9 24.9 - - + -
2114B SER 3.3 13.9 + - - +
2115B PRO* 3.2 13.9 - - + +
2117B LEU* 1.3 79.0 - - - +
2119B ARG* 1.3 63.3 + - - +
2121B MET* 3.4 9.7 + - + +
2122B PHE* 2.9 60.1 + - + -
3696B GLN* 4.8 9.6 - - + +
3700B HIS* 3.5 22.0 - - + +
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Residues in contact with ARG2119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2115B PRO* 2.9 20.6 + - - +
2116B GLU* 3.6 10.2 - - - +
2118B VAL* 1.3 78.0 - - - +
2120B ALA* 1.3 58.6 + - - +
2122B PHE* 3.3 4.0 + - - +
2123B SER* 2.8 31.9 + - - +
3700B HIS* 3.4 25.2 + - - +
3704B THR* 3.4 30.5 - - - +
3715B ASP* 5.9 1.0 - - - +
3717B LEU* 3.5 44.0 - - + +
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Residues in contact with ALA2120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1938B LEU* 5.5 8.7 - - + -
1941B CYS* 3.5 21.7 - - + -
2116B GLU 2.9 18.0 + - - +
2117B LEU* 3.7 6.3 - - - +
2119B ARG* 1.3 77.7 - - - +
2121B MET* 1.3 57.4 + - - +
2123B SER* 2.7 20.3 + - - -
2124B LEU* 2.9 20.4 + - - +
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Residues in contact with MET2121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937B LYS* 6.1 0.4 - - - -
1941B CYS* 4.0 14.6 - - + -
2103B VAL* 3.5 42.7 - - + +
2106B TRP* 3.9 35.4 - - + -
2107B ALA* 4.2 13.0 - - + +
2112B VAL* 5.4 4.3 - - + -
2117B LEU* 2.9 44.7 + - + +
2118B VAL* 3.7 12.8 - - + +
2120B ALA* 1.3 76.4 - - - +
2122B PHE* 1.3 66.4 + - + +
2124B LEU* 3.3 3.6 + - - +
2125B LEU* 2.9 29.3 + - - +
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Residues in contact with PHE2122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2107B ALA* 5.5 10.5 - - + -
2118B VAL* 2.9 44.6 + - + +
2119B ARG* 3.8 4.5 - - - +
2121B MET* 1.3 84.0 - - + +
2123B SER* 1.3 57.8 + - - +
2125B LEU* 3.3 9.6 + - + -
2126B HIS 2.9 13.2 + - - -
3673B LEU* 5.3 10.3 - - + -
3693B PRO 4.8 3.4 - - - -
3696B GLN* 4.3 9.4 - - + -
3697B LEU* 3.5 59.2 - - + -
3700B HIS* 4.6 16.4 - + + -
3701B PHE* 6.1 2.9 - + - -
3717B LEU* 5.6 5.6 - - + -
3721B TYR* 2.3 41.6 + + + +
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Residues in contact with SER2123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119B ARG* 2.8 17.2 + - - +
2120B ALA* 2.7 25.8 + - - -
2122B PHE* 1.3 74.2 - - - +
2124B LEU* 1.3 55.9 + - - +
2126B HIS* 3.3 8.4 + - - +
2127B ARG* 2.9 40.4 + - - +
3716B TYR* 4.8 15.3 - - - -
3717B LEU* 5.3 14.5 - - - +
3721B TYR* 5.2 1.6 - - - -
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Residues in contact with LEU2124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941B CYS* 3.2 43.5 - - - +
1944B LEU* 3.6 28.7 - - + +
1945B GLU* 4.0 13.7 - - + +
1948B CYS* 5.5 5.6 - - + -
2099B VAL* 3.5 29.2 - - + -
2103B VAL* 5.2 7.6 - - + -
2120B ALA 2.9 16.7 + - - +
2121B MET* 3.7 4.0 - - - +
2123B SER* 1.3 76.3 - - - +
2125B LEU* 1.3 58.1 + - - +
2127B ARG* 3.3 9.3 + - + +
2128B GLN* 2.9 31.5 + - + +
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Residues in contact with LEU2125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2099B VAL* 6.0 0.7 - - - -
2100B SER* 5.1 7.9 - - - +
2103B VAL* 3.7 31.3 - - + +
2104B VAL* 4.5 7.0 - - + -
2121B MET 2.9 17.4 + - - +
2122B PHE* 3.3 10.3 + - + +
2124B LEU* 1.3 78.3 - - - +
2126B HIS* 1.3 57.2 + - - +
2128B GLN* 4.1 4.2 - - - +
2129B TYR* 2.9 43.2 + - + +
3669B MET* 6.0 3.6 - - + +
3673B LEU* 4.4 30.5 - - + -
3721B TYR* 3.3 29.4 - - + +
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Residues in contact with HIS2126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2122B PHE 2.9 10.2 + - - +
2123B SER* 3.7 7.4 - - - +
2125B LEU* 1.3 79.0 - - - +
2127B ARG* 1.3 67.0 + - + +
2129B TYR* 5.1 1.6 - - - -
2130B ASP* 3.1 44.6 + - + +
3665B PHE* 4.9 1.7 - + - -
3716B TYR* 6.2 4.7 - + - -
3717B LEU* 6.2 0.9 - - - -
3720B ALA* 3.4 28.0 - - + +
3721B TYR* 3.3 29.1 + + + +
3724B ILE* 3.7 32.0 - - + +
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Residues in contact with ARG2127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734B TYR* 5.8 0.8 + - - -
1945B GLU* 5.2 8.1 + - - +
1948B CYS* 3.9 31.4 - - - +
1949B ASP* 2.5 36.1 + - - +
1952B LEU* 4.3 18.8 - - - +
2123B SER* 2.9 26.4 + - - +
2124B LEU* 3.3 8.5 + - + +
2126B HIS* 1.3 83.5 - - + +
2128B GLN* 1.3 59.7 + - - +
2130B ASP 3.1 19.4 - - - +
2131B GLY* 4.7 1.9 - - - -
2134B GLU* 5.1 10.5 - - - +
3716B TYR* 5.9 4.3 - - + -
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Residues in contact with GLN2128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1948B CYS* 5.0 7.4 - - + -
2043B CYS 5.6 1.4 - - - +
2095B LEU* 6.2 2.5 - - + -
2096B GLN* 4.0 32.4 - - + +
2099B VAL* 4.6 11.4 - - + -
2100B SER* 5.7 2.9 - - - +
2124B LEU* 2.9 28.0 + - + +
2125B LEU* 4.1 4.0 - - - +
2127B ARG* 1.3 77.4 - - - +
2129B TYR* 1.3 63.3 + - - +
2130B ASP 3.5 1.9 + - - -
2131B GLY* 4.7 1.7 + - - -
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Residues in contact with TYR2129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2096B GLN* 5.9 0.2 - - - -
2100B SER* 5.7 11.0 - - - -
2125B LEU* 2.9 28.2 + - + +
2126B HIS* 4.7 1.8 - - - +
2128B GLN* 1.3 77.6 - - - +
2130B ASP* 1.3 58.0 + - + +
2131B GLY 4.0 1.7 + - - -
3665B PHE* 3.5 45.3 + + + +
3668B ARG* 3.4 30.0 + - - +
3669B MET* 3.6 24.7 - - + -
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Residues in contact with ASP2130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126B HIS* 3.1 31.3 + - + +
2127B ARG* 3.1 17.2 - - - +
2128B GLN 4.6 0.2 - - - -
2129B TYR* 1.3 77.0 - - + +
2131B GLY* 1.3 61.4 + - - +
2132B LEU 3.7 0.9 - - - +
2133B GLY* 4.7 8.3 - - - +
2134B GLU* 3.9 11.7 + - - +
3665B PHE* 3.5 34.5 - - + -
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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
------------------------------------------------------------
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