Contacts of the strand formed by residues 1152 - 1158 (chain A) in PDB entry 3DKF
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 SER1152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1111A SER* 5.9 3.6 - - - -
1112A LEU 5.3 1.1 - - - -
1114A ARG* 3.7 23.6 - - - +
1146A CYS 4.0 0.3 - - - +
1147A LEU* 3.8 1.0 - - - -
1148A ARG* 3.0 41.7 + - - +
1149A SER 4.0 6.6 + - - -
1151A GLY* 1.3 72.5 - - - +
1153A PRO* 1.3 66.6 - - - +
1154A LEU* 3.8 5.9 + - - +
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Residues in contact with PRO1153 (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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1111A SER* 3.6 5.2 + - - -
1112A LEU* 3.0 44.5 + - + +
1113A ASN 3.4 25.6 - - - +
1115A ILE* 3.7 22.4 - - + -
1124A PHE* 3.7 28.5 - - + -
1146A CYS 3.3 6.1 - - - +
1147A LEU* 3.8 9.4 - - + -
1151A GLY 3.1 8.5 - - - +
1152A SER* 1.3 83.4 - - - +
1154A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU1154 (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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1076A LEU* 4.2 2.7 - - + -
1078A VAL* 3.8 25.1 - - + -
1080A PHE* 4.5 17.7 - - + -
1109A VAL* 3.8 20.0 - - + -
1110A LYS 3.3 1.6 - - - -
1111A SER* 3.7 31.2 - - - +
1124A PHE* 4.5 1.1 - - - -
1145A ILE* 3.6 4.3 - - - +
1146A CYS* 2.7 67.2 + - + +
1148A ARG* 6.1 4.0 - - + -
1152A SER* 4.6 5.4 - - - +
1153A PRO* 1.3 76.9 - - - +
1155A VAL* 1.3 63.8 + - - +
1156A VAL* 4.1 2.0 + - + -
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Residues in contact with VAL1155 (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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1108A ALA 3.5 1.9 - - - +
1109A VAL* 3.4 2.9 - - - -
1110A LYS* 2.7 47.7 + - + +
1112A LEU* 3.7 34.1 - - + -
1124A PHE* 4.1 9.2 - - + -
1142A LEU* 3.7 21.5 - - + -
1144A GLY 4.2 2.0 - - - -
1145A ILE* 4.9 0.7 - - - +
1154A LEU* 1.3 75.9 - - - +
1156A VAL* 1.3 62.0 + - - +
1157A LEU* 3.9 20.1 + - + +
1225A LEU* 4.0 33.7 - - + +
1226A ALA* 5.3 0.4 - - - -
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Residues in contact with VAL1156 (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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1071A ILE* 3.6 22.9 - - + -
1076A LEU* 3.7 33.4 - - + -
1097A LEU* 4.8 2.2 - - + -
1107A CYS* 3.8 28.3 - - + -
1108A ALA 3.5 2.9 - - - +
1109A VAL* 4.3 9.9 - - + -
1142A LEU* 3.7 3.8 - - - +
1143A LEU* 2.9 36.9 + - + +
1144A GLY 3.0 21.4 + - - +
1146A CYS* 5.0 1.6 - - + -
1154A LEU* 4.6 6.3 - - + +
1155A VAL* 1.3 76.2 - - - +
1157A LEU* 1.3 62.7 + - - +
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Residues in contact with LEU1157 (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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1A SX8 3.7 41.7 - - + +
1107A CYS* 3.3 6.6 - - - +
1108A ALA* 2.7 47.6 + - + +
1110A LYS* 5.0 8.1 - - + -
1131A MET* 4.1 18.4 - - + -
1140A LEU* 4.2 14.1 - - + -
1142A LEU* 4.1 17.9 - - + +
1143A LEU* 3.9 4.5 - - - -
1155A VAL* 3.9 27.4 - - + +
1156A VAL* 1.3 74.7 - - - +
1158A PRO* 1.3 73.0 - - + +
1226A ALA* 4.1 7.6 - - + -
1230A TYR* 5.4 0.2 - - - +
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Residues in contact with PRO1158 (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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1A SX8 3.6 15.6 - - - -
1106A HIS 4.9 1.1 - - - +
1140A LEU* 4.0 14.3 - - + +
1141A SER* 3.3 36.3 - - - +
1143A LEU* 3.9 22.0 - - + -
1157A LEU* 1.3 89.0 - - + +
1159A TYR* 1.3 63.5 + - - +
1160A MET* 3.6 22.8 + - + +
1219A LYS* 6.6 0.2 - - - -
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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