Contacts of the helix formed by residues 1092 - 1112 (chain B) in PDB entry 4X86
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 ALA1092 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088B ARG 3.8 4.5 + - - +
1089B ASP* 3.2 18.2 + - - +
1090B LEU 3.3 0.4 - - - -
1091B GLU* 1.3 76.6 - - - +
1093B PRO* 1.3 77.2 - - + +
1094B GLU* 3.2 9.0 - - - +
1095B VAL* 3.0 26.9 + - + +
1096B GLN* 3.1 11.1 + - - +
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Residues in contact with PRO1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1091B GLU 3.2 6.9 - - - +
1092B ALA* 1.3 84.6 - - + +
1094B GLU* 1.3 67.4 + - + +
1096B GLN* 3.9 4.1 - - + +
1097B GLU* 2.9 33.5 + - - +
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Residues in contact with GLU1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.8 14.8 - - + +
1092B ALA* 4.0 8.7 - - - +
1093B PRO* 1.3 90.1 - - + +
1095B VAL* 1.3 61.9 + - + +
1097B GLU* 4.0 4.4 - - - +
1098B SER* 3.0 30.0 + - - -
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Residues in contact with VAL1095 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A VAL* 4.3 1.8 - - + +
98A LEU* 4.4 23.3 - - + +
99A ILE* 4.4 14.1 - - + +
102A VAL* 4.3 13.7 - - + -
1064B LEU* 3.5 25.8 - - + -
1089B ASP 4.2 5.8 - - - +
1090B LEU* 3.8 16.8 - - + +
1092B ALA* 3.0 23.9 + - + +
1094B GLU* 1.3 80.4 - - + +
1096B GLN* 1.3 62.6 + - - +
1098B SER* 3.4 2.9 + - - -
1099B TYR* 3.1 22.5 + - - +
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Residues in contact with GLN1096 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1062B LEU 4.2 9.7 + - - +
1063B LEU* 4.9 6.7 - - - +
1064B LEU* 4.0 24.0 + - - +
1065B SER 5.4 0.2 + - - -
1090B LEU 4.2 8.9 + - - +
1091B GLU* 4.6 8.5 - - - +
1092B ALA 3.1 14.3 + - - +
1093B PRO* 4.0 5.4 - - + +
1095B VAL* 1.3 76.4 - - - +
1097B GLU* 1.3 58.6 + - - +
1099B TYR* 3.4 11.5 + - - +
1100B ARG* 3.0 28.9 + - + +
1203B SO4 4.1 23.4 + - - -
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Residues in contact with GLU1097 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1093B PRO 2.9 19.3 + - - +
1094B GLU* 4.0 4.7 - - - +
1096B GLN* 1.3 74.8 - - - +
1098B SER* 1.3 67.7 + - - +
1100B ARG* 2.5 50.9 + - - +
1101B GLN* 3.0 41.5 + - - +
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Residues in contact with SER1098 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 3.8 2.6 - - - -
95A VAL* 3.1 31.1 + - - +
98A LEU* 3.7 17.3 - - - +
1094B GLU 3.0 20.2 + - - -
1095B VAL 3.8 2.9 - - - -
1096B GLN 3.4 0.2 - - - -
1097B GLU* 1.3 76.9 - - - +
1099B TYR* 1.3 62.3 + - - +
1101B GLN* 3.4 12.2 + - - +
1102B GLN* 3.0 23.9 + - - +
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Residues in contact with TYR1099 (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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95A VAL* 3.6 21.7 - - + +
96A TRP* 5.7 4.7 - + - -
99A ILE* 5.0 2.0 - - + -
119A LEU* 6.2 1.8 - - + -
123A TYR* 4.3 29.2 - + - -
1060B PRO* 6.0 0.3 - - - +
1061B GLN* 2.6 32.2 + - - +
1062B LEU 3.7 17.5 - - - -
1064B LEU* 3.9 47.8 - - + -
1067B ALA* 4.3 11.5 - - + +
1095B VAL 3.1 14.5 + - - +
1096B GLN* 3.6 13.5 - - - +
1097B GLU 3.2 0.2 - - - -
1098B SER* 1.3 77.5 - - - +
1100B ARG* 1.3 65.2 + - - +
1102B GLN* 3.2 5.0 + - + +
1103B LEU* 2.9 37.9 + - + +
1203B SO4 5.1 0.4 - - - -
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Residues in contact with ARG1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1096B GLN* 3.0 20.1 + - - +
1097B GLU* 2.5 45.4 + - - +
1099B TYR* 1.3 76.6 - - - +
1101B GLN* 1.3 74.3 + - - +
1103B LEU* 3.4 5.7 + - - +
1104B ARG* 2.9 59.9 + - - +
1201B CPS 3.0 42.8 + - + +
1203B SO4 3.9 25.6 - - - +
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Residues in contact with GLN1101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1097B GLU* 3.0 41.6 + - - +
1098B SER* 3.7 11.9 - - - +
1100B ARG* 1.3 92.8 - - - +
1102B GLN* 1.3 64.1 + - - +
1104B ARG* 3.4 22.7 + - - +
1105B SER* 3.0 25.5 + - - -
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Residues in contact with GLN1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A SER* 5.1 4.7 - - - -
95A VAL* 4.0 29.6 + - + +
96A TRP* 4.6 13.8 + - + +
123A TYR* 3.4 23.3 + - + +
1098B SER 3.0 14.4 + - - +
1099B TYR* 3.2 9.8 + - + +
1101B GLN* 1.3 75.3 - - - +
1103B LEU* 1.3 58.6 + - - +
1105B SER* 3.3 7.7 + - - -
1106B ASP* 2.9 60.3 + - - +
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Residues in contact with LEU1103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 3.5 25.9 + - + +
127A LEU* 4.4 8.3 - - + -
1060B PRO* 4.6 13.2 - - + -
1061B GLN 4.2 13.9 - - - +
1062B LEU* 4.0 26.5 - - + -
1099B TYR* 2.9 30.2 + - + +
1100B ARG* 3.6 6.3 - - - +
1102B GLN* 1.3 78.9 - - - +
1104B ARG* 1.3 61.8 + - - +
1106B ASP* 3.9 0.3 - - - -
1107B ILE* 3.0 53.4 + - + +
1201B CPS 4.6 7.2 - - + -
1203B SO4 4.6 9.4 - - - +
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Residues in contact with ARG1104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1100B ARG* 2.9 45.3 + - - +
1101B GLN* 3.9 27.8 + - - +
1102B GLN 3.3 0.2 - - - -
1103B LEU* 1.3 75.7 - - - +
1105B SER* 1.3 62.7 + - - +
1107B ILE* 3.6 1.2 + - - +
1108B GLN* 3.2 46.8 + - - +
1201B CPS 3.6 47.4 - - + +
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Residues in contact with SER1105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1101B GLN 3.0 17.7 + - - -
1102B GLN* 3.6 8.9 + - - -
1104B ARG* 1.3 78.7 - - - +
1106B ASP* 1.3 65.3 + - - +
1108B GLN* 3.5 10.9 + - - +
1109B LYS* 3.1 38.2 + - - +
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Residues in contact with ASP1106 (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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123A TYR* 2.6 35.3 + - - +
124A GLU* 5.1 2.4 - - - +
127A LEU* 3.6 22.9 - - + -
1102B GLN* 2.9 38.4 + - - +
1103B LEU 4.0 1.6 - - - +
1105B SER* 1.3 76.9 + - - +
1107B ILE* 1.3 67.0 + - - +
1109B LYS* 3.4 18.9 + - - +
1110B ARG* 3.1 32.1 + - - +
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Residues in contact with ILE1107 (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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127A LEU* 4.4 4.9 - - + -
130A LEU* 4.0 20.9 - - + -
135A ILE* 3.9 26.7 - - + +
138A LEU* 4.2 13.9 - - + -
1060B PRO* 5.3 2.5 - - + -
1062B LEU* 6.2 0.4 - - + -
1103B LEU* 3.0 42.3 + - + +
1104B ARG 4.0 3.1 - - - +
1106B ASP* 1.3 75.9 - - - +
1108B GLN* 1.3 64.3 + - - +
1110B ARG* 3.3 5.5 + - - +
1111B LEU* 2.9 22.1 + - + +
1201B CPS 3.9 50.9 - - + -
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Residues in contact with GLN1108 (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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1104B ARG* 3.2 39.1 + - + +
1105B SER* 3.7 11.0 - - - +
1107B ILE* 1.3 78.8 - - - +
1109B LYS* 1.3 62.3 + - + +
1111B LEU* 3.3 10.6 + - - +
1112B GLN* 3.1 30.6 + - - +
1201B CPS 4.0 28.3 + - + +
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Residues in contact with LYS1109 (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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1105B SER* 3.1 35.2 + - - +
1106B ASP* 3.7 17.5 - - - +
1107B ILE 3.2 0.4 - - - -
1108B GLN* 1.3 75.9 - - + +
1110B ARG* 1.3 71.6 + - - +
1112B GLN* 3.1 36.4 + - - +
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Residues in contact with ARG1110 (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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124A GLU* 4.0 22.7 + - - +
127A LEU* 3.4 49.9 + - - +
128A SER* 4.2 16.0 + - - +
130A LEU* 5.6 5.6 - - + -
135A ILE* 5.8 1.8 - - + -
1106B ASP* 3.1 22.7 + - - +
1107B ILE* 3.9 5.2 - - - +
1109B LYS* 1.3 78.6 - - - +
1111B LEU* 1.3 61.7 + - - +
1112B GLN 3.0 5.4 + - - -
1113B GLU* 3.6 19.8 + - - +
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Residues in contact with LEU1111 (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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132A LEU* 6.1 4.0 - - + -
135A ILE* 3.8 30.7 - - + +
1107B ILE* 2.9 14.8 + - + +
1108B GLN* 3.3 15.9 - - - +
1109B LYS 3.2 0.2 - - - -
1110B ARG* 1.3 71.4 - - - +
1112B GLN* 1.3 56.2 + - - +
1113B GLU* 2.9 17.6 + - - -
1201B CPS 5.0 28.0 - - + -
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Residues in contact with GLN1112 (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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1108B GLN* 3.1 19.2 + - - +
1109B LYS* 3.2 31.1 - - - +
1110B ARG 3.0 1.6 - - - -
1111B LEU* 1.3 74.6 - - - +
1113B GLU* 1.3 57.4 + - - +
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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