Contacts of the strand formed by residues 1039 - 1051 (chain A) in PDB entry 2QOM
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 ALA1039 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1037A GLY 3.5 9.2 - - - +
1038A GLU* 1.3 80.1 - - - +
1040A GLY* 1.3 59.2 + - - +
1068A ASP* 3.8 9.9 - - - +
1069A LYS* 4.8 0.9 - - - +
1070A LYS* 5.7 0.2 - - - +
1297A ARG* 4.5 3.2 + - - -
1299A SER* 3.9 4.3 - - - -
1300A PHE* 2.8 56.2 + - + +
1301A GLY* 4.5 4.2 - - - +
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Residues in contact with GLY1040 (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 ALA* 1.3 78.9 - - - +
1041A ALA* 1.3 60.3 + - - +
1067A VAL* 3.3 7.6 - - - +
1068A ASP* 2.9 35.2 + - - +
1297A ARG* 3.9 20.2 - - - -
1298A TYR 3.7 9.2 - - - -
1299A SER* 4.4 1.1 - - - -
1300A PHE* 3.6 7.3 - - - -
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Residues in contact with ALA1041 (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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1040A GLY* 1.3 73.9 - - - +
1042A TRP* 1.3 65.1 + - - +
1066A GLY 3.4 10.1 - - - +
1067A VAL* 4.4 10.1 - - + -
1297A ARG* 3.5 3.6 - - - +
1298A TYR* 3.0 44.6 + - + +
1300A PHE* 4.1 8.9 - - + -
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Residues in contact with TRP1042 (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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1028A ARG* 3.3 45.3 - - + -
1029A MET* 3.9 19.6 - - + +
1041A ALA* 1.3 80.3 - - - +
1043A ALA* 1.3 72.4 + - - +
1044A ARG* 4.4 4.9 - - + -
1064A GLN* 3.5 33.0 - - + -
1065A VAL* 3.4 7.9 - - - +
1066A GLY* 2.9 54.1 + - - +
1067A VAL 4.2 0.4 - - - -
1068A ASP* 4.3 1.8 - - - -
1083A THR* 3.6 9.2 - - - -
1108A TYR* 3.2 36.6 + + - -
1295A ASN* 6.4 0.9 - - + -
1296A PHE* 3.1 16.2 - - - +
1297A ARG* 3.7 30.1 - - + +
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Residues in contact with ALA1043 (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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1042A TRP* 1.3 83.3 - - - +
1044A ARG* 1.3 60.8 + - - +
1064A GLN 3.3 6.7 - - - +
1065A VAL* 3.7 16.8 - - + -
1295A ASN* 3.4 2.4 - - - -
1296A PHE* 2.9 36.9 + - + +
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Residues in contact with ARG1044 (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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1024A ASN* 4.9 1.2 + - - +
1027A LYS* 3.2 24.2 - - - +
1028A ARG* 3.4 42.8 - - - +
1042A TRP* 4.3 2.2 - - + -
1043A ALA* 1.3 75.2 - - - +
1045A ILE* 1.3 68.5 + - - +
1046A MET* 4.3 9.0 - - - +
1062A HIS* 3.3 24.7 + - - +
1063A VAL* 3.5 5.0 - - - +
1064A GLN* 2.6 69.2 + - + +
1293A ASN* 3.1 25.0 + - - +
1294A ALA 3.2 12.8 - - - +
1295A ASN* 4.6 1.6 - - - +
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Residues in contact with ILE1045 (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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1044A ARG* 1.3 78.2 - - - +
1046A MET* 1.3 64.7 + - - +
1047A SER* 4.2 6.5 - - - +
1061A THR* 4.4 17.7 - - + -
1062A HIS 3.4 7.9 - - - +
1063A VAL* 4.0 16.6 - - + -
1292A VAL* 3.8 0.9 - - + +
1293A ASN* 3.4 2.6 - - - -
1294A ALA* 3.0 45.6 + - + +
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Residues in contact with MET1046 (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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1027A LYS* 4.5 18.2 - - - -
1044A ARG* 4.3 8.2 - - + +
1045A ILE* 1.3 77.6 - - - +
1047A SER* 1.3 63.9 + - - +
1060A TYR* 3.7 34.6 - - + +
1061A THR* 3.5 1.1 - - - -
1062A HIS* 2.7 63.1 + - + +
1291A ALA* 5.1 6.1 - - + -
1292A VAL 3.1 15.9 - - - +
1293A ASN* 3.7 21.3 - - - +
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Residues in contact with SER1047 (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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1045A ILE* 4.2 8.3 - - - +
1046A MET* 1.3 79.6 - - - +
1048A GLY* 1.3 58.7 + - - +
1060A TYR 3.3 10.8 + - - -
1061A THR* 4.0 13.8 + - - +
1291A ALA* 3.3 1.7 - - - -
1292A VAL* 2.7 42.4 + - - +
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Residues in contact with GLY1048 (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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1047A SER* 1.3 78.7 + - - +
1049A THR* 1.3 67.8 + - - -
1059A ASN* 3.3 2.1 - - - +
1060A TYR* 3.0 51.4 + - - +
1290A ASN* 3.3 14.6 - - - -
1291A ALA* 3.9 2.0 - - - -
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Residues in contact with THR1049 (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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1048A GLY* 1.3 77.2 + - - -
1050A GLY* 1.3 62.0 + - - +
1057A SER* 5.6 3.6 - - - -
1058A ASP* 3.1 20.0 - - - +
1059A ASN* 3.6 17.2 - - + +
1060A TYR* 4.1 3.8 - - - -
1286A TYR* 4.4 1.8 - - - -
1288A VAL* 3.7 3.4 - - - -
1289A ASP* 2.8 31.1 + - + +
1290A ASN* 2.9 25.8 + - - +
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Residues in contact with GLY1050 (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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1049A THR* 1.3 76.1 - - - +
1051A SER* 1.3 63.3 + - - -
1057A SER* 3.3 4.7 - - - -
1058A ASP* 2.9 40.8 + - - +
1286A TYR* 3.3 12.0 + - - -
1287A ASN 3.0 15.5 - - - -
1288A VAL* 4.1 0.7 - - - -
1289A ASP* 3.3 6.7 - - - +
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Residues in contact with SER1051 (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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1050A GLY* 1.3 75.0 - - - -
1052A ALA* 1.3 61.3 + - - +
1056A PHE 3.4 13.9 - - - -
1057A SER* 4.1 8.1 - - - +
1285A LYS 3.8 1.4 - - - +
1286A TYR* 3.4 7.9 - - - -
1287A ASN* 2.9 30.3 + - - +
1289A ASP* 2.9 25.3 + - - -
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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