Contacts of the helix formed by residues 1065 - 1080 (chain A) in PDB entry 6A5T
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 MET1065 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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847A GLU 3.4 18.6 - - - +
848A ASP* 3.2 39.5 - - - +
849A ILE 3.7 6.4 - - - +
850A MET* 3.7 15.5 - - - +
1063A GLY 2.8 7.1 + - - +
1064A GLU* 1.3 67.5 - - - +
1066A VAL* 1.3 51.8 + - - +
1067A GLY 2.7 16.9 + - - -
1068A VAL* 3.1 17.4 + - + +
1069A ILE* 4.0 5.1 + - - +
1427A VAL* 4.7 5.4 - - + -
1439A MET* 3.5 45.3 - - + -
1440A GLY 4.6 1.3 - - - +
1139B ILE* 4.0 27.8 - - + +
1140B ALA* 5.1 5.9 + - - -
1142B GLY* 5.3 3.5 - - - -
88F TYR* 5.2 0.4 + - - -
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Residues in contact with VAL1066 (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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849A ILE* 3.9 11.4 + - + +
851A VAL* 4.0 16.4 - - + -
857A THR* 5.4 1.1 - - + -
869A TYR* 3.3 51.4 - - + +
1060A VAL* 4.6 2.2 - - + -
1064A GLU* 2.3 47.5 + - + +
1065A MET* 1.3 64.9 - - - +
1067A GLY* 1.3 56.2 + - - +
1068A VAL 3.2 0.2 - - - -
1069A ILE* 2.7 39.8 + - + +
1070A ALA* 2.9 10.4 + - - +
1370A HIS* 4.7 0.9 - - - -
1373A LEU* 3.9 11.6 - - + +
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Residues in contact with GLY1067 (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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846A LEU* 3.8 20.5 - - - +
849A ILE* 3.6 18.6 + - - -
1065A MET 2.7 8.3 + - - -
1066A VAL* 1.3 78.9 - - - +
1068A VAL* 1.3 60.6 + - - -
1070A ALA* 3.0 6.3 + - - +
1071A ALA 3.0 17.7 + - - -
1373A LEU* 3.5 19.5 - - - -
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Residues in contact with VAL1068 (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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843A VAL* 4.5 15.5 - - + -
846A LEU* 4.5 1.5 + - - -
847A GLU* 4.0 27.8 - - + +
849A ILE 5.3 0.2 + - - -
1065A MET* 3.1 11.4 + - + +
1067A GLY* 1.3 76.4 - - - +
1069A ILE* 1.3 64.1 + - - +
1071A ALA* 3.0 8.2 + - - +
1072A GLN* 2.9 34.0 + - + +
1136B ASP* 3.7 23.8 - - - +
1139B ILE* 3.7 23.8 - - + -
1140B ALA* 3.8 14.6 - - + -
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Residues in contact with ILE1069 (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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453A LYS* 5.0 10.3 - - + +
515A PRO* 3.9 30.3 - - + -
1064A GLU* 3.6 28.0 - - + +
1065A MET 4.5 2.5 - - - +
1066A VAL* 2.7 33.5 + - + +
1068A VAL* 1.3 73.8 - - - +
1070A ALA* 1.3 59.3 + - - -
1072A GLN* 3.3 5.5 + - + +
1073A SER* 2.9 31.6 + - - +
1370A HIS* 3.4 21.1 - - + +
1140B ALA* 4.3 24.9 - - + +
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Residues in contact with ALA1070 (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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846A LEU* 4.6 6.5 - - + -
1066A VAL 2.9 4.9 + - - -
1067A GLY 3.1 9.9 - - - +
1069A ILE* 1.3 78.1 - - - +
1071A ALA* 1.3 65.7 + - - +
1073A SER 3.7 0.2 - - - -
1074A ILE* 3.0 33.7 + - + +
1370A HIS* 3.2 35.6 + - - +
1373A LEU* 3.9 24.0 - - + -
1374A LEU 5.2 1.3 - - - +
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Residues in contact with ALA1071 (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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839A GLN* 5.2 2.2 - - - +
842A LEU* 3.6 33.4 - - + +
843A VAL* 3.6 29.2 - - + -
846A LEU* 4.3 6.8 - - + +
1067A GLY 3.0 11.8 + - - +
1068A VAL* 3.6 8.3 - - - +
1070A ALA* 1.3 75.0 - - - +
1072A GLN* 1.3 65.0 + - - +
1074A ILE* 3.1 5.0 + - - +
1075A GLY* 2.9 21.5 + - - -
1374A LEU* 6.2 0.4 - - - -
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Residues in contact with GLN1072 (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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450A SER 4.7 1.0 + - - -
451A LEU 4.4 0.9 - - - +
452A HIS* 3.6 17.3 - - + +
453A LYS* 2.6 33.3 + - - +
839A GLN* 3.6 26.4 + - - +
843A VAL* 4.8 4.0 - - + -
1068A VAL* 2.9 24.7 + - + +
1069A ILE* 3.9 5.4 - - - +
1071A ALA* 1.3 79.3 - - - +
1073A SER* 1.3 60.1 + - - +
1076A GLU* 2.8 33.7 + - - +
1136B ASP* 3.7 29.9 + - - +
1137B CYS* 3.8 21.4 - - - +
1140B ALA* 4.5 2.8 - - - +
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Residues in contact with SER1073 (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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452A HIS* 5.2 6.1 - - - +
514A SER* 4.8 0.9 + - - -
515A PRO* 4.8 2.8 - - - +
516A GLN* 3.4 40.9 + - - +
1069A ILE* 2.9 23.1 + - - +
1070A ALA 3.7 2.5 - - - -
1072A GLN* 1.3 75.8 - - - +
1074A ILE* 1.3 62.2 + - - +
1076A GLU* 4.4 2.9 - - - +
1077A PRO* 3.6 18.7 - - - +
1366A VAL* 4.1 15.1 - - - +
1370A HIS* 5.2 7.2 - - - -
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Residues in contact with ILE1074 (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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842A LEU* 4.8 12.6 - - + -
1070A ALA* 3.0 24.4 + - + +
1071A ALA* 3.8 4.9 - - - +
1073A SER* 1.3 82.8 - - - +
1075A GLY* 1.3 65.2 + - - +
1076A GLU 3.3 0.4 - - - -
1077A PRO* 3.2 11.5 - - - +
1078A ALA* 3.4 11.3 + - - +
1103A LEU* 5.2 12.6 - - + -
1107A LEU* 6.0 0.9 - - + -
1355A ILE* 5.6 3.8 - - + -
1359A ILE* 3.5 30.6 - - + +
1366A VAL* 5.5 1.3 - - + -
1370A HIS* 4.2 20.9 - - + +
1371A MET* 4.7 7.4 - - + +
1374A LEU* 3.9 40.2 - - + -
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Residues in contact with GLY1075 (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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835A THR* 5.7 1.0 - - - +
838A ILE* 5.6 2.5 - - - -
839A GLN* 4.9 18.5 - - - +
842A LEU* 4.8 11.4 - - - +
1071A ALA 2.9 13.2 + - - -
1072A GLN 3.7 1.8 - - - -
1074A ILE* 1.3 79.2 - - - +
1076A GLU* 1.3 63.4 + - - +
1078A ALA* 3.0 12.2 + - - +
1079A THR* 2.9 22.8 + - - -
1103A LEU* 5.8 0.4 - - - -
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Residues in contact with GLU1076 (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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451A LEU* 4.0 13.7 - - + +
452A HIS* 3.6 33.4 + - + -
516A GLN* 2.8 39.1 + - - +
839A GLN* 5.0 1.9 + - - -
1072A GLN 2.8 19.6 + - - +
1073A SER* 4.4 2.5 - - - +
1075A GLY* 1.3 75.6 - - - +
1077A PRO* 1.3 63.5 - - + +
1079A THR* 2.6 38.0 + - - -
1080A GLN* 3.3 30.4 + - + +
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Residues in contact with PRO1077 (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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516A GLN* 3.1 26.7 - - - +
1073A SER 3.6 15.7 - - - +
1074A ILE 3.2 14.1 - - - +
1076A GLU* 1.3 97.9 - - + +
1078A ALA* 1.3 59.5 + - - +
1079A THR 3.5 0.2 + - - -
1080A GLN* 3.8 6.5 + - + +
1081A MET* 3.3 27.5 + - - +
1359A ILE* 5.0 11.4 - - + +
1364A SER* 4.8 19.7 + - - +
1366A VAL* 4.6 9.9 - - + -
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Residues in contact with ALA1078 (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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835A THR* 3.9 15.8 - - + +
838A ILE* 5.8 4.9 - - + -
1074A ILE 3.4 8.1 + - - +
1075A GLY* 3.0 20.5 + - - +
1077A PRO* 1.3 78.4 - - - +
1079A THR* 1.3 61.7 + - - +
1081A MET* 3.2 28.1 - - + +
1100A VAL* 4.0 5.8 - - + +
1103A LEU* 3.7 29.8 - - + -
1359A ILE* 6.0 1.5 - - + +
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Residues in contact with THR1079 (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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451A LEU* 3.9 28.1 - - + +
835A THR* 4.2 25.8 + - + +
839A GLN* 5.3 0.9 + - - -
1075A GLY 2.9 10.8 + - - -
1076A GLU* 2.6 23.6 + - - -
1078A ALA* 1.3 70.6 - - - +
1080A GLN* 1.3 65.7 + - + +
1081A MET* 2.8 14.8 + - - +
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Residues in contact with GLN1080 (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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480A ASN* 3.7 24.8 - - - +
1076A GLU* 3.3 27.4 + - - +
1077A PRO* 3.8 6.1 + - + +
1078A ALA 3.5 0.2 - - - -
1079A THR* 1.3 87.8 - - + +
1081A MET* 1.3 60.7 + - - +
1362A ASP* 5.2 1.0 - - - +
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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