Contacts of the strand formed by residues 1118 - 1123 (chain A) in PDB entry 2H7C
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 TYR1118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1052A GLY* 3.2 29.8 - - - -
1053A ILE 3.2 5.8 - - - +
1054A PRO* 3.6 28.4 - - + +
1055A PHE* 3.5 6.2 - - - -
1058A PRO* 4.8 4.1 - - + +
1084A PRO* 3.7 32.8 - - + -
1085A PRO* 4.3 8.3 - - + -
1115A ASP* 2.7 51.8 + - - -
1116A CYS* 2.9 19.7 + - - +
1117A LEU* 1.3 76.0 - - - +
1119A LEU* 1.3 62.0 + - - +
1149A ALA* 6.1 0.2 - - - -
1169A GLN* 3.1 29.1 + - - +
2184B HIS* 5.0 6.6 + - - -
2278B THR* 5.0 3.6 - - + +
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Residues in contact with LEU1119 (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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1052A GLY 3.6 0.5 + - - -
1053A ILE* 3.0 45.7 + - + +
1055A PHE* 3.9 23.8 - - + -
1118A TYR* 1.3 76.1 - - - +
1120A ASN* 1.3 66.4 + - - +
1121A ILE* 3.7 32.5 - - + -
1149A ALA* 5.6 0.9 - - - -
1166A VAL* 4.2 12.6 - - + -
1167A THR 3.2 14.1 - - - +
1168A ILE* 4.0 13.9 - - + -
1197A ALA* 4.4 10.5 - - + +
1200A TRP* 3.7 30.1 - - + -
1201A VAL* 4.8 0.9 - - + -
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Residues in contact with ASN1120 (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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1050A PHE 3.3 7.4 - - - +
1051A LEU* 3.4 22.8 - - + +
1052A GLY* 2.8 29.5 + - - -
1083A TYR* 4.7 0.2 - - - -
1084A PRO* 3.6 11.0 - - - +
1119A LEU* 1.3 75.7 - - - +
1121A ILE* 1.3 63.2 + - - +
1122A TYR* 4.0 11.3 + - + -
1149A ALA* 4.2 4.0 - - - +
1150A SER* 3.3 35.4 + - - +
1165A VAL 3.7 0.7 - - - +
1166A VAL* 3.3 6.1 - - - +
1167A THR* 2.9 47.9 + - - +
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Residues in contact with ILE1121 (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 ALA 3.7 0.3 - - - +
1049A ILE* 3.3 8.5 - - - +
1050A PHE* 2.8 44.9 + - + +
1053A ILE* 3.9 12.1 - - + -
1119A LEU* 3.7 13.5 - - + -
1120A ASN* 1.3 78.3 - - - +
1122A TYR* 1.3 69.8 + - - +
1123A THR* 4.0 3.6 - - - +
1164A VAL* 3.8 24.9 - - + -
1165A VAL 3.5 2.7 - - - +
1166A VAL* 4.2 8.5 - - + -
1200A TRP* 3.8 35.0 - - + -
1205A ILE* 4.3 6.3 - - + -
1208A PHE* 4.0 30.5 - - + -
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Residues in contact with TYR1122 (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 VAL* 4.2 5.8 - - + -
1048A ALA 3.7 4.3 - - - -
1049A ILE* 3.7 37.0 - - + -
1051A LEU* 3.8 15.0 - - + +
1083A TYR* 4.7 0.9 + - - -
1104A ARG* 4.0 13.2 + - - -
1120A ASN* 4.0 25.1 + - + +
1121A ILE* 1.3 77.7 - - - +
1123A THR* 1.3 59.5 + - - +
1150A SER* 5.6 0.5 - - - -
1152A TYR 3.7 11.3 + - - -
1153A ASP* 3.3 18.8 - - - -
1154A GLY* 3.4 34.8 - - - +
1155A LEU* 3.4 14.4 - - - -
1158A ALA* 3.7 9.8 - - + +
1164A VAL* 3.4 2.1 - - - -
1165A VAL* 2.8 45.5 + - + +
1167A THR* 4.3 10.1 - - + -
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Residues in contact with THR1123 (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 VAL* 3.8 3.3 - - - +
1048A ALA* 2.9 47.8 + - + +
1050A PHE* 4.3 10.5 - - + -
1121A ILE* 4.6 3.6 - - + -
1122A TYR* 1.3 74.9 - - - +
1124A PRO* 1.3 63.9 - - - +
1125A ALA* 3.2 16.4 + - - +
1127A LEU* 4.3 11.2 - - + -
1164A VAL* 3.6 15.6 - - - +
1208A PHE* 2.6 33.1 + - + +
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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