Contacts of the helix formed by residues 1063 - 1078 (chain M) in PDB entry 3HOU
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 MET1063 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846M GLU 3.3 27.8 - - - +
847M ASP* 4.5 4.0 - - - -
848M ILE 3.7 13.2 - - - +
849M MET* 3.5 19.5 - - + -
1061M GLY 3.5 7.2 - - - +
1062M GLU* 1.3 70.4 + - - +
1064M VAL* 1.3 63.3 + - - +
1065M GLY 3.0 5.3 + - - -
1066M VAL* 3.3 3.8 + - + +
1067M LEU* 3.2 20.0 + - - +
1424M VAL* 4.7 0.7 - - + -
1436M ILE* 3.2 45.1 - - + -
1139N ILE* 2.9 43.1 - - + +
1140N ALA* 4.3 10.4 + - - +
1142N GLY* 4.3 5.4 - - - -
88R TYR* 4.8 1.2 + - - -
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Residues in contact with VAL1064 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848M ILE* 3.5 9.7 + - + +
849M MET* 4.4 4.3 - - - -
850M VAL* 3.8 14.8 - - + +
856M THR* 4.6 1.6 - - + -
868M TYR* 3.1 54.1 + - + +
1058M VAL* 5.1 0.2 - - + -
1062M GLU* 2.7 30.5 + - + +
1063M MET* 1.3 70.6 - - - +
1065M GLY* 1.3 57.2 + - - +
1067M LEU* 3.6 9.2 - - + +
1068M ALA* 2.8 29.8 + - + +
1370M LEU* 4.0 21.3 - - + -
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Residues in contact with GLY1065 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845M LEU* 3.3 26.7 - - - +
848M ILE* 2.6 32.8 + - - -
1063M MET 3.0 1.2 + - - -
1064M VAL* 1.3 77.3 - - - +
1066M VAL* 1.3 63.0 + - - -
1068M ALA* 3.0 4.8 + - - +
1069M ALA* 2.9 20.8 + - - +
1370M LEU* 5.1 1.8 - - - -
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Residues in contact with VAL1066 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842M VAL* 4.6 11.2 - - + -
845M LEU 3.8 3.3 + - - -
846M GLU* 3.5 30.2 + - + +
1063M MET* 3.3 7.0 + - + +
1065M GLY* 1.3 72.5 - - - +
1067M LEU* 1.3 66.6 + - - +
1069M ALA* 3.1 7.8 + - - +
1070M GLN* 3.0 39.6 + - + +
1135N ARG* 5.9 0.2 - - - +
1136N ASP* 3.6 29.4 - - + +
1139N ILE* 3.8 25.8 - - + -
1140N ALA* 4.0 9.0 - - + -
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Residues in contact with LEU1067 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451M HIS* 6.3 2.0 - - + -
452M LYS* 4.1 22.7 - - + +
514M PRO* 4.0 34.3 - - + -
515M GLN* 5.0 2.0 - - + +
868M TYR* 4.6 9.0 - - - +
1062M GLU* 4.2 17.9 - - - +
1063M MET 3.2 11.7 + - - +
1064M VAL* 3.6 11.4 - - + +
1065M GLY 3.1 0.6 - - - -
1066M VAL* 1.3 80.6 - - - +
1068M ALA* 1.3 65.9 + - - +
1070M GLN* 3.1 9.7 + - + +
1071M SER* 2.9 36.9 + - - +
1367M HIS* 3.9 17.7 - - + -
1140N ALA* 4.9 8.8 - - + +
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Residues in contact with ALA1068 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845M LEU* 4.7 5.6 - - + -
868M TYR* 6.2 0.4 - - + -
1064M VAL* 2.8 22.0 + - + +
1065M GLY 3.4 3.6 - - - +
1067M LEU* 1.3 73.2 - - - +
1069M ALA* 1.3 65.5 - - - +
1071M SER* 3.2 9.5 + - - -
1072M ILE* 3.3 20.4 + - + +
1366M ARG 5.5 0.2 - - - -
1367M HIS* 3.5 41.4 + - - +
1370M LEU* 4.2 16.2 - - + -
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Residues in contact with ALA1069 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838M GLN* 5.9 0.9 - - - -
841M LEU* 3.6 13.3 - - + +
842M VAL* 3.7 40.2 - - + +
845M LEU* 3.7 16.9 - - + +
1065M GLY 2.9 11.8 + - - +
1066M VAL* 3.3 11.0 - - - +
1067M LEU 3.1 0.2 + - - -
1068M ALA* 1.3 79.1 - - - +
1070M GLN* 1.3 64.2 + - - +
1072M ILE* 3.0 5.1 + - - +
1073M GLY* 2.9 18.7 + - - -
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Residues in contact with GLN1070 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449M SER 4.7 2.0 + - - -
450M LEU 3.2 27.1 + - - +
451M HIS* 3.5 8.8 - - + +
452M LYS* 3.3 19.6 + - - +
515M GLN* 4.6 1.1 - - - -
838M GLN* 4.8 6.9 - - - +
842M VAL* 4.5 10.2 - - + +
1066M VAL* 3.0 31.6 + - + +
1067M LEU* 3.7 7.0 - - + +
1069M ALA* 1.3 74.6 - - - +
1071M SER* 1.3 58.5 + - - +
1073M GLY* 4.4 1.6 - - - +
1074M GLU* 2.9 36.7 + - - +
1136N ASP* 4.1 7.1 - - - +
1137N CYS* 3.8 30.9 - - - +
1140N ALA* 3.7 12.7 - - - +
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Residues in contact with SER1071 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515M GLN* 3.7 25.2 + - - +
1067M LEU* 2.9 29.2 + - - +
1068M ALA 3.4 5.4 - - - -
1069M ALA 3.2 0.4 - - - -
1070M GLN* 1.3 76.7 - - - +
1072M ILE* 1.3 57.3 + - - +
1075M PRO* 3.0 20.1 - - - +
1363M VAL* 3.5 13.0 - - - +
1367M HIS* 3.4 38.9 + - - -
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Residues in contact with ILE1072 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841M LEU* 3.8 16.2 - - + -
845M LEU* 5.8 0.2 - - + -
1068M ALA 3.4 16.6 - - - +
1069M ALA* 3.0 6.7 + - - +
1071M SER* 1.3 78.4 - - - +
1073M GLY* 1.3 64.5 - - - +
1075M PRO* 2.8 22.5 - - - +
1076M ALA* 3.3 7.8 + - + +
1101M LEU* 5.0 18.8 - - + -
1105M LEU* 6.5 0.2 - - + -
1352M VAL* 5.5 3.4 - - + -
1356M ILE* 4.2 20.8 - - + +
1363M VAL* 4.9 0.9 - - + -
1367M HIS* 4.2 7.9 - - + +
1368M MET* 4.2 26.9 - - + -
1371M LEU* 3.6 39.9 - - + -
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Residues in contact with GLY1073 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834M THR* 5.1 0.2 + - - -
837M ILE* 5.8 2.0 - - - -
838M GLN* 3.7 26.8 - - - +
841M LEU* 3.9 8.9 - - - +
1069M ALA 2.9 13.6 + - - -
1070M GLN 3.9 0.2 - - - -
1072M ILE* 1.3 78.5 - - - +
1074M GLU* 1.3 63.6 + - - +
1076M ALA* 2.8 21.0 + - - +
1077M THR* 3.1 12.6 + - - -
1101M LEU* 6.2 0.2 - - - -
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Residues in contact with GLU1074 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450M LEU* 3.8 25.6 - - + +
451M HIS* 3.1 41.3 + - + +
515M GLN* 3.1 22.2 + - - +
838M GLN* 4.4 3.2 - - - +
1070M GLN* 2.9 23.7 + - - +
1073M GLY* 1.3 69.8 - - - +
1075M PRO* 1.3 66.6 - - + +
1077M THR* 3.1 23.8 + - - -
1078M GLN* 3.5 25.2 + - - +
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Residues in contact with PRO1075 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515M GLN* 4.1 5.8 - - - +
1071M SER 3.0 25.4 - - - +
1072M ILE* 2.8 24.9 - - - +
1074M GLU* 1.3 97.2 - - + +
1076M ALA* 1.3 59.4 + - - +
1077M THR 3.1 0.2 - - - -
1078M GLN* 3.3 19.2 + - + +
1079M MET* 3.4 14.0 + - - +
1356M ILE* 4.9 7.9 - - + -
1359M ASP* 5.2 0.5 - - - +
1361M SER* 4.6 24.0 + - - +
1363M VAL* 4.1 13.0 - - + -
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Residues in contact with ALA1076 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834M THR* 3.0 16.4 + - - +
837M ILE* 5.8 4.0 - - + -
1072M ILE 3.3 11.6 + - - +
1073M GLY* 2.8 17.7 + - - +
1075M PRO* 1.3 73.8 - - - +
1077M THR* 1.3 62.5 + - - +
1079M MET* 3.1 43.2 + - + +
1098M VAL* 4.0 5.6 - - + +
1101M LEU* 4.0 17.9 - - + -
1356M ILE* 6.5 0.7 - - + -
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Residues in contact with THR1077 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448M PRO* 6.2 0.9 - - + -
450M LEU* 3.8 29.2 - - + +
834M THR* 3.2 29.5 + - + +
838M GLN* 4.8 3.6 - - - +
1073M GLY 3.1 12.7 + - - -
1074M GLU 3.2 11.2 + - - -
1076M ALA* 1.3 78.6 - - - +
1078M GLN* 1.3 72.4 + - - +
1079M MET 3.2 5.5 + - - -
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Residues in contact with GLN1078 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450M LEU* 4.6 4.9 - - - +
479M ASN* 4.7 20.5 + - - +
1074M GLU* 3.5 30.2 + - - +
1075M PRO* 3.3 13.0 + - + +
1076M ALA 3.2 0.8 - - - -
1077M THR* 1.3 101.6 - - - +
1079M MET* 1.3 57.1 + - - +
1080M THR* 3.1 15.2 + - - -
1359M ASP* 4.1 7.2 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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