Contacts of the helix formed by residues 1003 - 1012 (chain A) in PDB entry 3UGM
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 THR1003 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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997A CYS* 4.4 2.7 - - - -
1002A LEU* 1.3 79.6 - - - +
1004A LEU* 1.3 54.1 + - - +
1005A ASP* 2.7 9.3 + - - +
1006A GLN* 2.6 64.8 + - - +
1007A VAL* 3.3 8.2 + - - +
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Residues in contact with LEU1004 (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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966A HIS* 2.9 28.9 - - + +
967A GLY* 3.2 17.7 - - - +
968A LEU* 3.7 20.9 - - + +
993A LEU* 3.7 25.1 - - + -
997A CYS* 4.2 11.4 - - - -
1003A THR* 1.3 68.0 - - - +
1005A ASP* 1.3 65.6 + - - +
1006A GLN 3.4 0.4 - - - -
1007A VAL* 3.0 25.3 - - - +
1008A VAL* 3.3 13.7 + - - +
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Residues in contact with ASP1005 (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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972A GLN* 3.1 27.1 + - - -
1003A THR* 2.7 12.8 + - - +
1004A LEU* 1.3 79.2 - - - +
1006A GLN* 1.3 57.9 + - - -
1008A VAL* 3.7 11.9 - - + +
1009A ALA* 3.5 18.7 - - - +
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Residues in contact with GLN1006 (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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1002A LEU* 3.3 26.1 - - + +
1003A THR* 2.6 50.7 + - - +
1005A ASP* 1.3 72.1 - - - +
1007A VAL* 1.3 65.4 + - - +
1008A VAL 3.4 0.2 - - - -
1009A ALA* 3.2 13.5 + - - +
1010A ILE* 3.2 24.4 + - + +
1037A PRO 5.5 2.6 + - - -
1041A VAL* 4.4 20.1 + - + +
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Residues in contact with VAL1007 (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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968A LEU* 5.7 3.6 - - + -
989A VAL* 3.7 17.7 - - + +
992A LEU* 5.5 1.3 - - + +
993A LEU* 4.0 26.0 - - + +
996A LEU* 4.6 15.9 - - + -
997A CYS* 5.2 4.5 - - - -
1002A LEU* 4.7 9.0 - - + +
1003A THR 3.3 4.5 + - - +
1004A LEU* 3.0 30.5 - - + +
1006A GLN* 1.3 76.8 - - - +
1008A VAL* 1.3 78.9 + - + +
1010A ILE* 2.8 10.6 + - - +
1011A ALA* 2.7 24.8 + - - +
1019A LEU* 3.7 21.1 - - + -
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Residues in contact with VAL1008 (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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968A LEU* 4.8 4.7 - - + -
972A GLN* 3.6 38.1 - - + +
975A ALA* 5.3 1.8 - - + -
976A ILE* 3.6 31.4 - - + -
989A VAL* 5.5 0.4 - - - -
1004A LEU 3.3 15.2 + - - +
1005A ASP* 3.7 17.5 - - + +
1007A VAL* 1.3 81.5 - - + +
1009A ALA* 1.3 59.6 + - + +
1010A ILE 2.9 0.2 + - - -
1011A ALA* 3.5 5.8 - - - -
1012A SER* 2.6 44.4 + - - -
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Residues in contact with ALA1009 (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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1005A ASP 3.5 17.9 - - - +
1006A GLN* 3.2 10.2 + - - +
1007A VAL 3.1 1.0 - - - -
1008A VAL* 1.3 82.6 - - + +
1010A ILE* 1.3 60.1 + - - +
1012A SER* 4.5 4.9 - - - -
1013A ASN* 3.4 20.5 - - - +
1042A ALA* 4.3 8.0 - - + +
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Residues in contact with ILE1010 (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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996A LEU* 6.5 0.2 - - + -
1002A LEU* 5.1 7.6 - - + -
1006A GLN* 3.4 19.5 - - + +
1007A VAL* 2.8 8.3 + - - +
1009A ALA* 1.3 79.1 - - - +
1011A ALA* 1.3 57.6 + - - +
1012A SER 2.8 3.6 - - - -
1013A ASN* 2.8 4.9 + - + +
1014A GLY 2.7 10.9 + - - +
1015A GLY 2.5 28.4 + - - -
1018A ALA* 3.8 17.0 - - + +
1019A LEU* 3.8 36.6 - - + +
1022A VAL* 4.4 24.0 - - + -
1041A VAL* 5.0 7.4 - - + -
1042A ALA* 3.7 30.3 - - + +
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Residues in contact with ALA1011 (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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976A ILE* 3.4 36.4 - - + +
979A ASN* 4.9 3.6 + - - +
981A GLY* 5.7 0.2 - - - -
985A ALA* 3.6 5.5 - - - +
989A VAL* 3.5 28.0 - - + -
1007A VAL 2.7 19.1 + - - +
1008A VAL* 3.6 4.7 - - - +
1010A ILE* 1.3 72.7 - - - +
1012A SER* 1.3 58.6 + - - +
1015A GLY* 3.3 23.1 + - - -
1019A LEU* 4.1 7.9 - - + +
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Residues in contact with SER1012 (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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975A ALA* 2.3 40.8 + - - +
976A ILE* 4.3 7.2 - - - +
979A ASN* 3.4 22.0 + - - +
1008A VAL* 2.6 26.6 + - - -
1009A ALA* 4.5 4.3 - - - -
1011A ALA* 1.3 74.5 - - - +
1013A ASN* 1.3 57.3 + - - +
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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