Contacts of the helix formed by residues 2114 - 2130 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1934D GLU* 5.4 8.4 - - - +
2112D VAL* 3.1 28.4 - - - +
2113D GLN* 1.3 80.2 - - - +
2115D PRO* 1.3 69.8 - - - +
2116D GLU* 3.9 3.3 + - - +
2117D LEU* 3.3 27.9 + - - +
2118D VAL* 3.3 10.8 + - - +
3703D ARG* 6.3 0.4 - - - -
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Residues in contact with PRO2115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2113D GLN 4.7 1.8 - - - +
2114D SER* 1.3 84.1 - - - +
2116D GLU* 1.3 62.8 + - + +
2118D VAL* 3.2 9.8 - - + +
2119D ARG* 2.9 33.5 + - - +
3700D HIS* 3.3 15.0 - - + +
3703D ARG* 4.9 25.3 - - + +
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Residues in contact with GLU2116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1938D LEU* 4.9 13.8 - - + +
2114D SER* 3.5 3.0 + - - +
2115D PRO* 1.3 82.9 - - + +
2117D LEU* 1.3 58.7 + - - +
2119D ARG* 3.3 12.3 + - - +
2120D ALA* 2.9 30.7 + - - +
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Residues in contact with LEU2117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1934D GLU* 3.2 43.1 - - + +
1937D LYS* 3.6 19.5 - - + -
1938D LEU* 4.0 19.9 - - + +
1941D CYS* 5.1 0.8 - - + +
2112D VAL* 3.5 24.7 - - + -
2114D SER* 3.3 19.3 + - - +
2116D GLU* 1.3 78.8 - - - +
2118D VAL* 1.3 55.7 + - - +
2120D ALA* 3.3 6.8 + - - +
2121D MET* 2.9 57.7 + - + +
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Residues in contact with VAL2118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2112D VAL* 3.9 24.9 - - + -
2114D SER 3.3 14.6 + - - +
2115D PRO* 3.2 13.5 - - + +
2117D LEU* 1.3 79.3 - - - +
2119D ARG* 1.3 63.1 + - - +
2121D MET* 3.7 9.0 - - + +
2122D PHE* 2.9 61.1 + - + -
3696D GLN* 4.8 9.0 - - + +
3700D HIS* 3.5 22.4 - - + +
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Residues in contact with ARG2119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2115D PRO* 2.9 20.0 + - - +
2116D GLU* 3.6 10.3 - - - +
2118D VAL* 1.3 78.4 - - - +
2120D ALA* 1.3 58.3 + - - +
2122D PHE* 3.3 4.2 + - - +
2123D SER* 2.8 31.5 + - - +
3700D HIS* 3.4 25.5 + - - +
3704D THR* 3.4 30.5 - - - +
3715D ASP* 5.9 0.6 - - - +
3717D LEU* 3.5 43.9 - - + +
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Residues in contact with ALA2120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1938D LEU* 5.5 8.7 - - + -
1941D CYS* 3.5 22.1 - - + -
2116D GLU 2.9 17.6 + - - +
2117D LEU* 3.3 6.0 + - - +
2119D ARG* 1.3 77.4 - - - +
2121D MET* 1.3 58.4 + - - +
2123D SER* 2.7 19.7 + - - -
2124D LEU* 2.9 20.6 + - - +
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Residues in contact with MET2121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1937D LYS* 6.1 0.2 - - - -
1941D CYS* 4.0 15.3 - - + -
2103D VAL* 3.5 43.9 - - + +
2106D TRP* 3.9 37.0 - - + -
2107D ALA* 4.2 12.6 - - + +
2112D VAL* 5.4 4.0 - - + -
2117D LEU* 2.9 42.3 + - + +
2118D VAL* 3.7 12.8 - - + +
2119D ARG 3.3 0.2 - - - -
2120D ALA* 1.3 77.4 - - - +
2122D PHE* 1.3 65.1 + - + +
2124D LEU* 3.3 3.3 + - - +
2125D LEU* 2.9 29.3 + - - +
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Residues in contact with PHE2122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2107D ALA* 5.5 10.3 - - + -
2118D VAL* 2.9 45.4 + - + +
2119D ARG* 3.8 4.3 - - - +
2121D MET* 1.3 83.1 - - + +
2123D SER* 1.3 57.8 + - - +
2125D LEU* 3.3 9.9 + - + +
2126D HIS* 2.9 13.5 + - - +
3673D LEU* 5.3 10.3 - - + -
3693D PRO 4.8 4.0 - - - -
3696D GLN* 4.3 10.1 - - + -
3697D LEU* 3.5 57.7 - - + -
3700D HIS* 4.6 15.9 - + + -
3701D PHE* 6.1 2.7 - + - -
3717D LEU* 5.6 4.7 - - + -
3721D TYR* 2.3 40.8 + + + +
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Residues in contact with SER2123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2119D ARG* 2.8 17.4 + - - +
2120D ALA* 2.7 25.1 + - - -
2122D PHE* 1.3 74.3 - - - +
2124D LEU* 1.3 56.2 + - - +
2126D HIS* 3.3 7.4 + - - +
2127D ARG* 2.9 39.4 + - - +
3716D TYR* 4.8 15.5 - - - -
3717D LEU* 5.3 14.5 - - - +
3721D TYR* 4.9 2.4 - - - -
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Residues in contact with LEU2124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1941D CYS* 3.2 43.5 - - - +
1944D LEU* 3.6 28.3 - - + +
1945D GLU* 4.0 15.0 - - + +
1948D CYS* 5.5 5.6 - - + -
2099D VAL* 3.5 29.2 - - + -
2103D VAL* 5.2 7.0 - - + -
2120D ALA 2.9 16.5 + - - +
2121D MET* 3.7 4.3 - - - +
2123D SER* 1.3 76.2 + - - +
2125D LEU* 1.3 58.2 + - - +
2127D ARG* 3.3 8.8 + - + +
2128D GLN* 2.9 31.0 + - + +
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Residues in contact with LEU2125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2099D VAL* 6.0 0.9 - - - -
2100D SER* 5.1 7.9 - - - +
2103D VAL* 3.7 32.2 - - + +
2104D VAL* 4.5 6.7 - - + -
2121D MET 2.9 16.5 + - - +
2122D PHE* 3.6 10.5 - - + +
2124D LEU* 1.3 77.4 - - - +
2126D HIS* 1.3 57.7 + - - +
2128D GLN* 4.1 4.2 - - - +
2129D TYR* 2.9 43.4 + - + +
3669D MET* 6.0 3.4 - - + +
3673D LEU* 4.4 30.1 - - + -
3721D TYR* 3.3 29.4 - - + +
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Residues in contact with HIS2126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2122D PHE 2.9 10.5 + - - +
2123D SER* 3.7 6.1 - - - +
2125D LEU* 1.3 78.3 - - - +
2127D ARG* 1.3 67.8 + - + +
2129D TYR* 5.1 1.6 - - - -
2130D ASP* 3.1 44.2 + - + +
3665D PHE* 4.9 2.4 - + - -
3716D TYR* 6.2 4.7 - + - -
3717D LEU* 6.2 0.4 - - - -
3720D ALA* 3.4 29.4 - - + +
3721D TYR* 3.3 29.5 + + + +
3724D ILE* 3.8 29.7 - - + +
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Residues in contact with ARG2127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1734D TYR* 5.8 0.8 + - - -
1945D GLU* 5.2 8.1 + - - +
1948D CYS* 3.9 30.7 - - - +
1949D ASP* 2.5 36.5 + - - +
1952D LEU* 4.3 19.4 - - - +
2123D SER* 2.9 27.0 + - - +
2124D LEU* 3.8 8.7 - - + +
2126D HIS* 1.3 83.1 - - + +
2128D GLN* 1.3 60.0 + - - +
2130D ASP 3.1 19.6 - - - +
2131D GLY* 4.7 1.9 - - - -
2134D GLU* 5.1 9.4 - - - +
3716D TYR* 5.9 4.3 - - + -
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Residues in contact with GLN2128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1948D CYS* 5.0 7.6 - - + -
2043D CYS 5.6 1.6 - - - +
2095D LEU* 6.1 2.2 - - + -
2096D GLN* 4.0 32.1 - - + +
2099D VAL* 4.6 12.1 - - + -
2100D SER* 5.7 2.9 - - - +
2124D LEU* 2.9 28.7 + - + +
2125D LEU* 4.1 3.1 - - - +
2127D ARG* 1.3 77.8 - - - +
2129D TYR* 1.3 63.2 + - - +
2130D ASP 3.5 2.3 + - - -
2131D GLY* 4.7 1.7 + - - -
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Residues in contact with TYR2129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2100D SER* 5.7 10.3 - - - -
2125D LEU* 2.9 25.9 + - + +
2126D HIS* 4.7 2.0 - - - +
2128D GLN* 1.3 77.3 - - - +
2130D ASP* 1.3 57.9 + - + +
2131D GLY 4.0 1.5 + - - -
3665D PHE* 3.5 45.5 + + + +
3668D ARG* 3.4 30.2 + - - +
3669D MET* 3.6 25.1 - - + -
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Residues in contact with ASP2130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2126D HIS* 3.1 31.2 + - + +
2127D ARG* 3.1 17.3 - - - +
2128D GLN 4.6 0.2 - - - -
2129D TYR* 1.3 76.4 - - + +
2131D GLY* 1.3 62.0 + - - +
2132D LEU 3.7 1.3 - - - +
2133D GLY* 4.7 8.3 - - - +
2134D GLU* 3.9 11.7 + - - +
3665D PHE* 3.5 34.3 - - + -
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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
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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