Contacts of the helix formed by residues 1071 - 1083 (chain B) in PDB entry 1RPM
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 THR1071 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1069B HIS* 3.0 19.8 + - - +
1070B ALA* 1.3 76.7 - - - +
1072B GLY* 1.3 57.5 + - - +
1074B LEU* 3.3 5.4 + - - +
1075B GLY* 2.9 25.6 + - - -
1153B GLU* 2.7 29.4 + - - +
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Residues in contact with GLY1072 (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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1034B GLU* 3.5 32.3 + - - +
1035B TYR* 5.0 4.5 - - - -
1058B PHE* 3.7 8.7 - - - -
1069B HIS* 4.2 4.6 + - - +
1070B ALA 3.3 0.4 - - - -
1071B THR* 1.3 78.2 - - - +
1073B LEU* 1.3 56.6 + - - +
1075B GLY* 3.2 2.9 + - - -
1076B PHE* 2.9 26.5 + - - +
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Residues in contact with LEU1073 (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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997B VAL* 4.8 6.1 - - + -
1034B GLU* 4.4 0.2 + - - -
1058B PHE* 3.7 34.2 - - + -
1061B TRP* 3.7 15.7 - - + -
1067B PRO* 5.4 1.6 - - + -
1069B HIS 5.1 1.2 + - - +
1070B ALA 3.2 8.0 + - - +
1072B GLY* 1.3 72.1 - - - +
1074B LEU* 1.3 59.1 + - - +
1076B PHE* 3.3 24.1 + - + +
1077B VAL* 2.9 40.0 + - + +
1104B CYS* 5.1 2.0 - - + -
1105B PHE* 5.1 10.3 - - + +
1108B ILE* 3.7 21.8 - - + -
1146B PHE* 3.2 39.0 - - + -
1150B ALA* 5.6 0.7 - - + -
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Residues in contact with LEU1074 (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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1070B ALA* 2.9 16.4 + - + +
1071B THR* 3.4 9.0 - - + +
1073B LEU* 1.3 75.2 - - + +
1075B GLY* 1.3 65.0 + - - +
1077B VAL* 3.3 5.8 + - + +
1078B ARG* 3.2 26.3 + - - +
1108B ILE* 4.2 21.5 - - + -
1112B LEU* 4.6 6.9 - - + +
1150B ALA* 3.2 35.0 - - + +
1153B GLU* 3.6 27.4 - - + +
1154B ALA* 3.6 28.9 - - + +
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Residues in contact with GLY1075 (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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1035B TYR* 4.8 7.4 + - - -
1071B THR 2.9 14.9 + - - -
1072B GLY* 3.2 4.0 + - - -
1074B LEU* 1.3 78.6 - - - +
1076B PHE* 1.3 60.4 + - - +
1078B ARG* 3.4 7.0 + - - +
1079B GLN* 3.2 20.1 + - - +
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Residues in contact with PHE1076 (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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995B ILE* 3.8 22.2 - - + -
996B MET 4.4 0.4 - - - -
997B VAL* 4.3 4.0 - - + -
1035B TYR* 3.7 36.2 - + + -
1056B PHE* 3.2 52.7 - + + -
1057B HIS 4.0 1.6 - - - -
1058B PHE* 3.6 34.1 - + + -
1072B GLY 2.9 14.1 + - - +
1073B LEU* 3.3 22.9 - - + +
1075B GLY* 1.3 76.6 - - - +
1077B VAL* 1.3 62.3 + - - +
1079B GLN* 3.2 5.8 + - - +
1080B VAL* 3.0 27.8 + - + +
1105B PHE* 4.1 15.7 - + - -
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Residues in contact with VAL1077 (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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1073B LEU* 2.9 37.7 + - + +
1074B LEU* 3.3 7.6 + - - +
1076B PHE* 1.3 74.4 - - - +
1078B ARG* 1.3 57.5 + - - +
1080B VAL* 3.1 5.0 + - - +
1081B LYS* 2.9 34.2 + - + +
1105B PHE* 4.3 26.2 - - + -
1108B ILE* 4.2 20.4 - - + -
1109B ASP* 3.6 33.0 - - + +
1112B LEU* 4.1 17.7 - - + -
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Residues in contact with ARG1078 (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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1074B LEU 3.2 12.0 + - - +
1075B GLY* 3.8 9.6 - - - +
1076B PHE 3.4 0.2 - - - -
1077B VAL* 1.3 77.4 - - + +
1079B GLN* 1.3 59.7 + - - +
1081B LYS* 3.4 42.3 - - + +
1082B SER* 2.9 45.9 + - - +
1112B LEU* 5.5 7.2 - - + -
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Residues in contact with GLN1079 (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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1030B GLU* 4.3 10.5 + - - -
1032B LEU* 4.5 3.4 - - - +
1035B TYR* 2.7 33.4 + - + +
1037B ILE* 3.6 24.3 - - + +
1056B PHE* 4.1 7.9 - - + -
1075B GLY 3.2 12.8 + - - +
1076B PHE* 3.2 10.7 + - - +
1078B ARG* 1.3 73.1 - - - +
1080B VAL* 1.3 61.2 + - - +
1082B SER* 3.0 7.2 + - - -
1083B LYS* 2.9 61.3 + - + +
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Residues in contact with VAL1080 (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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995B ILE* 4.1 22.4 - - + -
1056B PHE* 3.6 40.6 - - + -
1076B PHE* 3.0 20.3 + - + +
1077B VAL 3.5 6.3 - - - +
1079B GLN* 1.3 77.5 - - - +
1081B LYS* 1.3 57.4 + - + +
1084B SER* 2.6 47.4 + - - +
1091B LEU* 4.2 9.9 - - + -
1105B PHE* 4.1 25.8 - - + -
1109B ASP* 6.1 0.2 - - - +
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Residues in contact with LYS1081 (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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1077B VAL* 2.9 23.2 + - + +
1078B ARG* 3.4 36.3 - - - +
1080B VAL* 1.3 77.6 - - + +
1082B SER* 1.3 63.7 + - - +
1084B SER* 3.8 14.8 + - - +
1109B ASP* 2.5 61.0 + - - +
1112B LEU* 3.7 24.8 - - + +
1113B ASP* 3.5 19.0 + - - +
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Residues in contact with SER1082 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078B ARG* 2.9 37.2 + - - +
1079B GLN* 3.0 18.0 + - - -
1081B LYS* 1.3 79.9 - - - +
1083B LYS* 1.3 70.2 + - - +
1084B SER 4.6 2.3 - - - +
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Residues in contact with LYS1083 (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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1028A GLU* 4.1 5.2 - - - +
1030A GLU* 6.2 0.2 - - - +
1083A LYS* 5.6 12.2 - - - +
1030B GLU* 3.4 17.0 + - - -
1037B ILE* 3.3 33.3 - - + +
1054B ARG* 2.8 49.6 + - - +
1056B PHE* 3.8 13.5 - - + -
1079B GLN* 2.9 40.0 + - - +
1082B SER* 1.3 82.6 + - - +
1084B SER* 1.3 60.8 + - - +
1085B PRO* 3.4 5.4 - - - +
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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
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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