Contacts of the helix formed by residues 1073 - 1090 (chain A) in PDB entry 3MP1
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 GLN1073 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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907A PHE* 3.7 21.1 - - + -
916A ILE* 3.3 43.2 - - + +
1071A ILE* 3.1 12.9 - - + +
1072A PRO* 1.3 95.2 - - - +
1074A MET* 1.3 58.6 + - - +
1075A SER 3.3 0.9 - - - -
1076A ALA* 3.3 9.9 + - - +
1077A PHE* 2.9 28.1 + - - +
1106A ALA 3.6 5.4 - - - +
1107A ALA* 4.2 16.8 - - - +
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Residues in contact with MET1074 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A ASP* 3.7 22.9 - - + +
804A ARG* 5.5 2.0 - - + -
906A ALA* 5.4 0.9 - - + -
907A PHE* 3.9 25.8 - - - -
996A PHE* 4.8 2.9 - - + -
1068A MET* 4.5 3.4 - - + -
1069A PRO* 3.6 49.1 - - + +
1071A ILE* 3.2 20.2 + - + +
1072A PRO 3.1 2.0 - - - -
1073A GLN* 1.3 78.4 - - - +
1075A SER* 1.3 57.6 + - - +
1077A PHE* 3.4 13.4 - - + +
1078A TRP* 3.0 70.5 + - + +
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Residues in contact with SER1075 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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804A ARG* 3.0 35.6 + - - +
1072A PRO 3.7 12.3 + - - -
1074A MET* 1.3 75.0 - - - +
1076A ALA* 1.3 67.5 + - - +
1078A TRP* 3.3 2.8 + - - +
1079A TYR* 3.1 33.7 + - - -
1110A PHE* 3.9 19.9 - - - -
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Residues in contact with ALA1076 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1072A PRO 5.6 0.2 - - - +
1073A GLN* 3.3 13.5 + - - +
1075A SER* 1.3 80.4 + - - +
1077A PHE* 1.3 64.7 + - - +
1079A TYR* 3.2 8.4 + - - +
1080A ALA* 3.1 23.0 + - - +
1105A ASN 3.7 10.4 - - - +
1106A ALA 3.7 10.1 - - - +
1107A ALA 4.7 1.6 - - - -
1108A ALA 3.7 23.1 - - - +
1110A PHE* 4.0 19.7 - - + -
1126A LEU* 5.5 2.0 - - + -
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Residues in contact with PHE1077 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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896A TRP* 3.8 17.3 - + - -
906A ALA* 3.5 33.7 - - + -
907A PHE* 4.0 16.8 - + + -
919A VAL* 5.3 0.2 - - + -
921A VAL* 3.7 23.6 - - + -
996A PHE* 4.4 2.9 - + - -
1073A GLN 2.9 16.9 + - - +
1074A MET* 3.4 14.1 - - + +
1076A ALA* 1.3 79.3 - - - +
1078A TRP* 1.3 102.5 + + - +
1080A ALA* 3.3 1.7 + - - +
1081A VAL* 3.2 45.2 + - + +
1106A ALA* 3.4 28.2 + - + +
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Residues in contact with TRP1078 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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803A ASP* 2.8 26.5 + - - -
804A ARG* 3.8 18.8 - - - +
892A PRO* 3.7 35.0 - - + +
893A TYR* 4.1 19.3 - + - -
896A TRP* 5.0 7.6 - + - -
996A PHE* 3.7 24.9 - + - -
1068A MET* 3.8 23.1 - - - -
1074A MET* 3.0 43.1 + - + +
1075A SER 3.8 3.8 - - - +
1076A ALA 3.3 0.2 - - - -
1077A PHE* 1.3 93.5 - + - +
1079A TYR* 1.3 58.5 + - - +
1081A VAL* 4.7 1.8 - - + +
1082A ARG* 3.0 31.4 + - - +
2B GLC 3.7 33.1 - - - +
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Residues in contact with TYR1079 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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783A GLU* 2.7 47.4 + - + +
804A ARG* 5.7 6.7 - - - -
1075A SER* 3.1 30.7 + - - -
1076A ALA* 3.2 8.2 + - - +
1078A TRP* 1.3 77.2 - - - +
1080A ALA* 1.3 59.3 + - - +
1082A ARG* 3.7 31.6 + - - +
1083A THR* 3.0 32.6 + - - -
1110A PHE* 3.8 26.4 - + - -
1123A ALA* 3.9 11.0 - - - +
1124A PRO* 3.6 45.5 - - + -
1126A LEU* 6.4 0.7 - - + -
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Residues in contact with ALA1080 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1076A ALA 3.1 15.5 + - - +
1077A PHE 3.7 4.7 - - - +
1079A TYR* 1.3 75.2 - - - +
1081A VAL* 1.3 60.9 + - + +
1083A THR* 3.3 5.9 + - - -
1084A ALA* 2.9 28.1 + - - +
1102A ALA* 3.4 35.9 - - + +
1105A ASN* 3.9 21.1 - - + +
1106A ALA* 4.0 2.7 - - + +
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Residues in contact with VAL1081 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A PRO* 3.7 21.5 - - + +
896A TRP* 4.4 20.6 - - + -
899A ILE* 4.8 4.9 - - + -
921A VAL* 4.7 8.5 - - + -
1077A PHE* 3.2 49.0 + - + +
1078A TRP* 4.3 2.5 - - + +
1080A ALA* 1.3 74.4 - - + +
1082A ARG* 1.3 62.1 + - - +
1084A ALA* 3.1 6.3 + - + +
1085A VAL* 2.8 46.1 + - + +
1099A LEU* 5.9 6.1 - - + -
1102A ALA* 4.9 3.6 - - + -
1106A ALA* 6.0 0.9 - - + -
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Residues in contact with ARG1082 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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780A LYS* 5.2 8.9 - - - +
783A GLU* 4.5 7.5 + - - -
890A GLN 3.4 25.6 - - - +
891A GLU* 4.5 10.4 + - - -
892A PRO* 3.5 22.1 - - + +
1078A TRP 3.0 20.6 + - - +
1079A TYR* 3.7 38.4 + - - +
1081A VAL* 1.3 77.4 - - - +
1083A THR* 1.3 68.3 + - - +
1085A VAL* 4.2 1.7 - - - +
1086A ILE* 3.2 36.5 + - + +
1121A PRO* 6.0 3.8 - - - +
1123A ALA 5.2 3.8 + - - -
1124A PRO* 5.2 1.8 - - - +
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Residues in contact with THR1083 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079A TYR 3.0 20.5 + - - -
1080A ALA* 3.5 7.2 - - - +
1081A VAL 3.1 0.6 - - - -
1082A ARG* 1.3 86.3 + - - +
1084A ALA* 1.3 61.6 + - - +
1086A ILE* 4.1 2.5 - - - +
1087A ASN* 3.1 46.7 + - - +
1093A GLN* 5.4 1.8 - - - +
1188A PRO* 5.9 8.6 - - + +
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Residues in contact with ALA1084 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930A LEU* 4.5 2.4 - - + +
1080A ALA 2.9 16.6 + - - +
1081A VAL* 3.7 5.6 - - + +
1083A THR* 1.3 76.9 - - - +
1085A VAL* 1.3 59.9 + - + +
1087A ASN* 4.6 0.7 - - - -
1088A ALA* 2.9 33.1 + - - +
1093A GLN* 5.2 0.2 - - - -
1098A ALA* 3.5 39.3 - - + +
1099A LEU* 4.2 11.9 - - + +
1102A ALA* 3.8 9.4 - - + -
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Residues in contact with VAL1085 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A LEU* 4.1 17.5 - - + +
892A PRO* 4.6 10.1 - - + -
895A THR* 3.9 20.9 - - - +
899A ILE* 4.3 18.2 - - + -
930A LEU* 4.4 20.5 - - + +
933A LEU* 4.6 8.1 - - + -
1081A VAL* 2.8 39.1 + - + +
1082A ARG* 4.2 4.0 - - - +
1084A ALA* 1.3 71.8 - - + +
1086A ILE* 1.3 67.0 + - + +
1088A ALA* 4.3 0.3 - - - +
1089A ALA* 3.2 26.8 + - + +
1099A LEU* 6.3 1.1 - - + -
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Residues in contact with ILE1086 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A LEU 4.0 17.7 - - - +
890A GLN* 3.9 37.9 - - + +
944A ALA* 5.8 0.2 - - - +
1082A ARG* 3.2 30.5 + - + +
1083A THR* 4.3 3.6 - - - +
1085A VAL* 1.3 76.7 - - + +
1087A ASN* 1.3 62.5 + - - +
1089A ALA* 4.1 3.6 - - - +
1090A SER* 2.9 26.8 + - - -
1092A ARG* 3.5 22.0 - - - +
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Residues in contact with ASN1087 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083A THR* 3.1 35.3 + - - +
1084A ALA 4.0 2.2 - - - +
1086A ILE* 1.3 81.0 - - - +
1088A ALA* 1.3 66.7 + - - +
1090A SER* 3.2 16.0 + - - -
1091A GLY 3.3 6.9 + - - -
1092A ARG* 3.4 35.8 + - + +
1093A GLN* 3.1 39.4 + - + +
1098A ALA* 4.7 0.2 - - + -
1189A GLY* 5.1 12.2 - - - -
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Residues in contact with ALA1088 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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930A LEU* 3.6 26.7 - - + -
934A VAL* 3.7 27.5 - - + +
1084A ALA 2.9 21.1 + - - +
1085A VAL 4.3 1.1 - - - +
1087A ASN* 1.3 73.5 - - - +
1089A ALA* 1.3 61.5 + - - +
1090A SER 3.4 0.5 + - - -
1091A GLY* 3.5 8.3 + - - -
1093A GLN 3.3 19.0 - - - +
1095A VAL* 4.3 7.4 - - + -
1098A ALA* 4.3 8.4 - - + +
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Residues in contact with ALA1089 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889A LEU* 5.2 7.0 - - + +
930A LEU* 6.2 0.7 - - + -
933A LEU* 5.5 4.0 - - + -
934A VAL* 4.3 9.6 - - + +
937A ILE* 3.4 40.2 - - + +
944A ALA* 3.7 20.7 - - + +
1085A VAL* 3.2 23.5 + - + +
1086A ILE* 4.2 3.8 - - - +
1088A ALA* 1.3 78.6 - - - +
1090A SER* 1.3 57.7 + - - +
1091A GLY 3.4 0.6 + - - -
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Residues in contact with SER1090 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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944A ALA* 4.6 10.3 - - - -
1086A ILE* 2.9 22.6 + - - -
1087A ASN 3.2 8.1 + - - -
1089A ALA* 1.3 76.1 - - - +
1091A GLY* 1.3 56.4 + - - +
1092A ARG* 3.1 46.1 + - - +
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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