Contacts of the helix formed by residues 1050 - 1069 (chain B) in PDB entry 3P8C
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 SER1050 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993B TYR* 5.3 1.2 + - - -
1044B PHE* 4.6 2.1 - - - +
1049B GLY* 1.3 71.4 - - - -
1051B ILE* 1.3 64.2 + - - +
1052B GLU* 3.9 5.5 + - - +
1053B ASP* 3.4 35.6 + - - -
1054B ARG* 3.1 34.7 + - - +
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Residues in contact with ILE1051 (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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971B ILE* 3.5 31.2 - - + -
1040B ALA* 4.2 2.7 - - + +
1041B ALA* 3.7 26.0 - - - +
1044B PHE* 4.1 22.0 - - + +
1045B THR* 3.7 12.6 - - - +
1049B GLY 4.0 1.1 + - - +
1050B SER* 1.3 68.9 + - - +
1052B GLU* 1.3 67.4 + - - +
1054B ARG* 3.2 4.7 + - - +
1055B LEU* 3.0 34.5 + - + +
1097B PHE* 3.7 37.9 - - + -
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Residues in contact with GLU1052 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050B SER* 4.2 6.5 - - - +
1051B ILE* 1.3 78.9 - - - +
1053B ASP* 1.3 60.5 + - - +
1055B LEU* 3.4 1.7 + - - +
1056B LYS* 2.9 49.5 + - + +
1097B PHE* 3.7 46.2 - - + +
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Residues in contact with ASP1053 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050B SER* 3.4 24.2 + - - +
1051B ILE 3.3 0.4 - - - -
1052B GLU* 1.3 80.5 - - - +
1054B ARG* 1.3 79.9 + - - +
1056B LYS* 3.3 14.6 + - - +
1057B GLU* 2.9 29.3 + - - +
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Residues in contact with ARG1054 (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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881B ARG* 3.6 12.2 - - - +
993B TYR* 3.7 14.9 + - - +
997B CYS* 3.6 27.6 - - - +
1000B MET* 4.9 8.6 - - + +
1040B ALA* 5.7 0.4 - - + -
1044B PHE* 3.6 42.6 - - + -
1050B SER* 3.1 25.9 + - - +
1051B ILE 3.8 2.0 - - - +
1053B ASP* 1.3 105.6 + - - +
1055B LEU* 1.3 58.0 - - + +
1057B GLU* 2.6 34.9 + - - +
1058B PHE* 2.9 25.8 + - - +
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Residues in contact with LEU1055 (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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1000B MET* 5.2 1.6 - - - -
1036B ILE* 4.1 25.6 - - + +
1037B ASN* 3.8 11.0 - - + +
1040B ALA* 3.8 26.2 - - + -
1051B ILE* 3.0 24.1 + - + +
1052B GLU* 3.9 3.8 - - - +
1054B ARG* 1.3 74.3 - - - +
1056B LYS* 1.3 53.3 + - - +
1058B PHE* 3.1 11.1 + - + +
1059B LEU* 2.8 35.9 + - - +
1091B ILE* 5.8 0.7 - - + -
1095B SER* 3.7 20.6 - - - +
1097B PHE* 3.8 24.5 - - + -
1098B LEU* 4.0 22.4 - - + +
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Residues in contact with LYS1056 (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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1052B GLU* 2.9 48.6 + - + +
1053B ASP* 3.5 14.1 - - - +
1055B LEU* 1.3 76.5 - - - +
1057B GLU* 1.3 61.6 + - - +
1059B LEU* 3.4 2.7 + - - +
1060B ALA* 3.0 24.4 + - - +
1097B PHE 5.0 0.9 - - - +
1098B LEU* 4.1 9.4 - - + +
1102B LEU* 3.6 42.2 - - + +
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Residues in contact with GLU1057 (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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881B ARG* 2.9 46.9 + - - +
997B CYS 5.8 1.1 - - - -
1000B MET* 6.4 2.0 - - - -
1001B VAL* 4.3 8.7 - - - +
1053B ASP 2.9 15.8 + - - +
1054B ARG* 2.6 40.6 + - - +
1055B LEU 3.3 0.2 - - - -
1056B LYS* 1.3 75.8 - - - +
1058B PHE* 1.3 63.5 + - - +
1060B ALA* 3.4 6.4 + - - +
1061B LEU* 3.2 28.2 + - + +
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Residues in contact with PHE1058 (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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1000B MET* 3.2 35.6 - - + +
1003B VAL* 3.8 12.3 - - + -
1004B ALA* 3.4 34.5 - - + +
1007B LEU* 4.2 8.3 - - + -
1036B ILE* 3.6 47.3 - - + -
1054B ARG 2.9 15.7 + - - +
1055B LEU* 3.1 18.4 + - + +
1057B GLU* 1.3 75.9 - - - +
1059B LEU* 1.3 58.1 + - + +
1061B LEU* 3.3 6.4 + - - +
1062B ALA* 2.8 43.7 + - + +
1091B ILE* 4.2 19.1 - - + -
1098B LEU* 5.8 0.4 - - + -
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Residues in contact with LEU1059 (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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1055B LEU 2.8 19.7 + - - +
1056B LYS 3.8 4.5 - - - +
1058B PHE* 1.3 76.6 - - + +
1060B ALA* 1.3 54.2 - - - +
1062B ALA* 3.7 1.7 - - + +
1063B SER* 2.8 45.0 + - - +
1088B LEU* 3.9 26.9 - - + +
1091B ILE* 4.8 6.7 - - + -
1092B VAL* 4.0 28.0 - - + -
1098B LEU* 3.9 29.2 - - + -
1102B LEU* 4.2 16.8 - - + -
1103B LEU* 4.2 14.1 - - + +
1106B CYS* 4.1 15.9 - - - -
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Residues in contact with ALA1060 (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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884B PHE* 6.6 0.4 - - + -
1056B LYS 3.0 17.4 + - - +
1057B GLU* 3.7 7.2 - - - +
1058B PHE 3.3 0.2 - - - -
1059B LEU* 1.3 75.8 - - - +
1061B LEU* 1.3 57.8 + - - +
1063B SER* 4.0 1.9 - - - -
1064B SER* 3.1 29.8 + - - -
1106B CYS* 4.7 15.6 - - + +
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Residues in contact with LEU1061 (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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880B MET 4.8 2.9 - - - +
881B ARG* 5.5 2.0 - - - -
884B PHE* 3.9 24.0 - - + +
890B MET* 3.8 25.4 - - + -
1001B VAL* 3.7 43.3 - - + -
1004B ALA* 4.0 6.5 - - + -
1005B VAL* 4.0 14.8 - - + -
1057B GLU* 3.2 19.3 + - + +
1058B PHE* 3.7 4.0 - - - +
1060B ALA* 1.3 76.2 - - - +
1062B ALA* 1.3 58.2 + - - +
1064B SER* 3.7 8.3 - - - +
1065B SER* 2.7 39.7 + - - +
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Residues in contact with ALA1062 (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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1004B ALA* 3.8 16.0 - - + +
1007B LEU* 4.2 13.2 - - + -
1058B PHE* 2.8 39.1 + - + +
1059B LEU* 3.7 4.0 - - - +
1061B LEU* 1.3 73.5 - - - +
1063B SER* 1.3 62.8 + - - +
1065B SER* 3.4 1.4 + - - -
1066B LEU* 3.0 28.4 + - - +
1088B LEU* 3.8 19.7 - - + -
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Residues in contact with SER1063 (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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1059B LEU* 2.8 31.8 + - - +
1060B ALA 4.0 2.7 - - - -
1062B ALA* 1.3 72.4 - - - +
1064B SER* 1.3 57.6 + - - +
1066B LEU* 3.3 1.0 + - - +
1067B LEU* 2.8 37.0 + - - +
1088B LEU* 4.0 16.9 - - - +
1103B LEU* 4.5 0.3 - - - +
1106B CYS* 3.4 41.9 - - - -
1107B PHE* 3.9 11.4 - - - +
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Residues in contact with SER1064 (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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365A ARG* 5.2 3.9 + - - +
884B PHE 4.5 10.6 + - - -
1060B ALA 3.1 19.7 + - - -
1061B LEU* 3.7 11.9 - - - +
1063B SER* 1.3 76.7 - - - +
1065B SER* 1.3 64.1 + - - +
1067B LEU* 3.3 10.6 + - - +
1068B LYS* 3.2 42.0 + - - +
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Residues in contact with SER1065 (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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890B MET* 5.5 1.6 - - - +
1004B ALA 3.8 12.9 + - - -
1005B VAL* 3.9 19.1 - - - +
1008B PRO* 3.7 28.4 - - - +
1061B LEU* 2.7 25.2 + - - +
1062B ALA 3.7 3.8 - - - -
1064B SER* 1.3 75.3 + - - +
1066B LEU* 1.3 61.8 + - - +
1068B LYS* 3.5 27.7 + - - +
1069B ILE* 3.9 5.2 + - - +
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Residues in contact with LEU1066 (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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1007B LEU* 4.2 11.9 - - + -
1008B PRO* 3.7 30.5 - - + -
1062B ALA 3.0 17.7 + - - +
1063B SER 3.9 2.7 - - - +
1065B SER* 1.3 73.8 - - - +
1067B LEU* 1.3 67.2 + - - +
1068B LYS 3.2 0.4 - - - -
1069B ILE* 3.0 24.3 - - + +
1084B VAL* 3.7 39.7 - - + +
1085B TYR* 3.0 36.4 + - + -
1087B LEU* 5.8 0.4 - - + -
1088B LEU* 3.7 32.8 - - + -
1107B PHE* 4.4 4.3 - - + -
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Residues in contact with LEU1067 (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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361A SER* 3.7 19.5 - - - +
364A ALA* 3.8 31.2 - - + +
365A ARG* 4.0 24.8 - - + -
1063B SER 2.8 25.4 + - - +
1064B SER* 3.3 7.6 + - - +
1066B LEU* 1.3 75.2 - - - +
1068B LYS* 1.3 58.0 + - - +
1070B GLY* 3.0 21.1 + - - -
1071B GLN* 4.3 1.6 + - - +
1085B TYR* 4.4 2.9 - - - +
1106B CYS 3.4 23.8 - - - +
1107B PHE* 3.6 24.2 - - + -
1108B PRO* 4.6 0.2 - - + -
1111B LEU* 3.7 21.1 - - + -
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Residues in contact with LYS1068 (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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365A ARG* 3.8 26.7 - - - +
884B PHE 4.9 5.6 + - - -
887B PRO* 4.1 24.0 + - + +
890B MET* 3.5 35.8 - - - +
891B ALA* 5.3 0.6 - - - +
1064B SER* 3.2 29.3 + - - +
1065B SER* 3.5 17.4 + - - +
1066B LEU 3.2 0.4 - - - -
1067B LEU* 1.3 77.9 - - - +
1069B ILE* 1.3 62.5 + - + +
1070B GLY 3.3 0.9 + - - -
1071B GLN* 3.7 12.5 + - - +
1072B GLU* 4.2 8.1 + - - +
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Residues in contact with ILE1069 (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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1008B PRO* 4.2 20.9 - - + +
1011B ALA* 4.1 23.3 - - + -
1065B SER 3.9 3.3 + - - +
1066B LEU* 3.0 38.6 - - + +
1068B LYS* 1.3 75.8 - - + +
1070B GLY* 1.3 52.0 + - - +
1071B GLN 3.2 1.8 - - - -
1072B GLU* 3.2 25.3 + - + +
1077B THR* 5.0 15.7 - - + +
1078B THR* 3.9 3.7 - - + +
1081B ARG* 2.8 53.3 + - + -
1085B TYR* 4.0 3.4 - - + +
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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
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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