Contacts of the helix formed by residues 1056 - 1068 (chain A) in PDB entry 3Q71
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 PRO1056 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1051A LEU* 4.3 10.1 - - + -
1055A GLY* 1.4 80.2 - - - +
1057A GLU* 1.3 76.5 + - - +
1058A LEU 3.0 1.1 + - - -
1059A GLN* 3.1 15.6 + - + +
1060A GLU* 3.2 28.1 + - - +
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Residues in contact with GLU1057 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1054A ALA 4.2 3.8 - - - +
1055A GLY* 3.5 7.4 - - - -
1056A PRO* 1.3 100.0 - - - +
1058A LEU* 1.3 56.2 + - - +
1060A GLU* 3.6 20.8 + - + +
1061A GLU* 2.8 32.6 + - - +
1082A TRP* 3.4 50.4 - - + +
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Residues in contact with LEU1058 (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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1033A ASN* 5.3 0.2 - - - +
1041A LEU* 3.8 20.2 - - + -
1047A SER 5.5 0.2 - - - +
1050A LEU* 4.0 25.1 - - + +
1051A LEU* 4.2 4.9 - - + +
1054A ALA* 3.9 23.6 - - + -
1055A GLY 3.0 14.9 + - - +
1057A GLU* 1.3 77.3 - - - +
1059A GLN* 1.3 57.2 + - - +
1061A GLU* 3.9 1.5 - - - +
1062A LEU* 2.9 31.5 + - - +
1079A THR* 3.3 26.5 - - - +
1080A SER 3.6 13.5 - - - +
1081A SER* 4.9 0.2 - - - -
1082A TRP* 4.1 10.8 - - + +
1084A LEU* 4.8 3.1 - - + -
1089A VAL* 4.3 10.3 - - + -
1091A HIS* 4.0 15.3 - - + +
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Residues in contact with GLN1059 (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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1039A LEU 2.9 23.4 + - - -
1040A VAL* 3.6 7.3 - - - +
1041A LEU* 2.7 39.2 + - - +
1042A SER* 4.5 0.9 + - - -
1051A LEU* 4.1 17.7 - - + +
1056A PRO* 3.1 10.6 + - + +
1058A LEU* 1.3 81.1 - - - +
1060A GLU* 1.3 58.5 + - + +
1062A LEU* 3.8 2.4 - - - +
1063A ASP* 3.0 56.9 + - - +
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Residues in contact with GLU1060 (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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1056A PRO* 3.2 31.5 + - - +
1057A GLU* 3.2 22.9 + - + +
1059A GLN* 1.3 77.4 - - + +
1061A GLU* 1.3 59.6 + - - +
1063A ASP* 3.5 7.0 + - - +
1064A THR* 2.8 30.2 + - - -
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Residues in contact with GLU1061 (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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1057A GLU 2.8 15.9 + - - +
1058A LEU 4.1 2.0 - - - +
1060A GLU* 1.3 75.6 - - - +
1062A LEU* 1.3 65.4 + - - +
1064A THR* 3.2 9.6 + - + -
1065A VAL* 3.0 29.1 + - + +
1078A LYS 4.6 1.4 - - - +
1079A THR* 3.5 14.1 - - + -
1080A SER* 2.6 49.1 + - - -
1082A TRP* 2.8 19.1 + - + +
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Residues in contact with LEU1062 (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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1035A VAL* 4.3 4.0 - - + -
1039A LEU* 3.7 30.4 - - + +
1041A LEU* 3.5 33.0 - - + -
1058A LEU 2.9 20.2 + - - +
1059A GLN* 3.8 5.8 - - - +
1061A GLU* 1.3 76.3 - - - +
1063A ASP* 1.3 57.5 + - - +
1065A VAL* 3.1 3.9 + - + +
1066A GLY* 2.9 25.6 + - - -
1077A LEU* 3.7 35.2 - - + -
1079A THR* 3.7 10.9 - - + +
1091A HIS* 3.7 27.4 - - + +
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Residues in contact with ASP1063 (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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1038A ASP 4.5 3.6 - - - +
1039A LEU* 4.0 18.3 - - - +
1059A GLN* 3.0 46.6 + - - +
1060A GLU* 3.8 6.6 - - - +
1061A GLU 3.3 0.2 - - - -
1062A LEU* 1.3 75.5 - - - +
1064A THR* 1.3 62.4 + - - +
1066A GLY* 3.5 1.1 + - - +
1067A GLN* 3.3 28.6 + - - +
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Residues in contact with THR1064 (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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1060A GLU 2.8 20.7 + - - -
1061A GLU* 3.3 14.7 - - + -
1062A LEU 3.2 0.2 - - - -
1063A ASP* 1.3 74.2 - - - +
1065A VAL* 1.3 69.8 + - + +
1067A GLN* 3.2 23.0 + - - +
1068A GLY 4.3 1.6 + - - -
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Residues in contact with VAL1065 (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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1061A GLU* 3.0 26.4 + - + +
1062A LEU* 3.1 8.3 + - + +
1064A THR* 1.3 79.2 - - + +
1066A GLY* 1.3 62.0 + - - +
1067A GLN 3.3 1.0 + - - -
1068A GLY* 3.8 6.9 + - - -
1069A VAL* 4.0 14.5 - - + +
1077A LEU* 3.9 29.4 - - + -
1078A LYS 3.5 24.0 - - - +
1079A THR* 4.6 2.5 - - + -
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Residues in contact with GLY1066 (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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1039A LEU* 3.8 20.4 - - - -
1062A LEU 2.9 15.2 + - - -
1063A ASP 3.5 2.0 + - - -
1064A THR 3.2 0.2 - - - -
1065A VAL* 1.3 75.7 - - - +
1067A GLN* 1.3 59.7 + - - +
1068A GLY 3.4 0.2 - - - -
1069A VAL* 2.9 28.9 - - - +
1071A VAL* 4.2 5.2 - - - +
1077A LEU* 3.9 11.0 - - - +
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Residues in contact with GLN1067 (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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1063A ASP* 3.3 16.3 + - + +
1064A THR* 3.2 14.9 + - - +
1065A VAL 3.2 1.6 - - - -
1066A GLY* 1.3 77.6 - - - +
1068A GLY* 1.3 61.3 + - - +
1069A VAL 3.5 2.3 + - - +
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Residues in contact with GLY1068 (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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1064A THR 4.3 1.8 + - - -
1065A VAL 3.8 4.6 + - - -
1066A GLY 3.4 0.6 - - - -
1067A GLN* 1.3 78.2 - - - +
1069A VAL* 1.3 65.6 + - - +
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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