Contacts of the strand formed by residues 1099 - 1104 (chain C) in PDB entry 2X4Y
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 TYR1099 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090C TRP* 4.0 2.5 - - - -
1091C ALA* 2.9 33.7 + - - +
1097C PRO* 4.0 9.0 - - + +
1098C SER* 1.3 73.6 - - - +
1100C PRO* 1.3 86.1 - - + +
1101C ALA 3.4 0.3 + - - -
1147C PHE* 3.7 23.4 - + + -
1149C ASP* 3.2 29.4 - - + +
1184C ILE* 6.4 0.7 - - + -
1187C SER* 2.9 33.9 + - - -
1188C VAL* 3.9 23.8 - - + -
1191C ALA* 3.4 22.7 - - + +
1194C ARG* 5.1 0.2 + - - -
2205C SO4 3.1 17.1 + - - -
36D M3L 3.7 29.6 - - - -
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Residues in contact with PRO1100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089C VAL 3.5 7.4 - - - +
1090C TRP* 3.5 24.9 - - + -
1099C TYR* 1.3 100.7 - - + +
1101C ALA* 1.4 59.7 + - - +
1147C PHE* 3.6 0.5 - - - -
1148C PHE* 3.1 21.3 + - + -
1165C LEU* 3.6 17.0 - - + -
1188C VAL* 3.9 8.1 - - + +
1191C ALA* 3.8 24.2 - - + +
1192C TYR* 3.6 26.0 - - - +
1195C ALA* 4.2 5.8 - - + -
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Residues in contact with ALA1101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088C LEU* 3.5 5.5 - - - +
1089C VAL* 2.8 33.0 + - + +
1091C ALA* 4.0 12.8 - - + -
1100C PRO* 1.4 76.3 - - - +
1102C LEU* 1.3 62.2 + - - +
1145C VAL* 3.8 21.8 - - + -
1146C LEU 3.3 14.1 - - - +
1147C PHE* 3.9 14.6 - - + -
1148C PHE* 3.6 12.7 - - - -
1165C LEU* 4.8 0.6 - - - +
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Residues in contact with LEU1102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086C LEU* 3.4 36.1 - - + +
1087C ASP 3.7 4.3 - - - +
1088C LEU* 3.8 15.9 - - + -
1101C ALA* 1.3 75.8 - - - +
1103C ILE* 1.3 70.2 + - - +
1104C ILE* 3.5 21.9 + - + +
1120C ILE* 4.5 11.0 - - + -
1121C PRO* 5.3 2.2 - - + -
1145C VAL* 3.3 4.3 - - - -
1146C LEU* 2.9 39.7 + - + +
1148C PHE* 4.0 12.3 - - + -
1152C ARG* 5.0 9.2 - - - +
1198C HIS* 3.8 31.2 - - + +
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Residues in contact with ILE1103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083C LEU* 3.6 33.4 - - + -
1084C ASP 3.6 16.2 - - - +
1085C ALA* 4.0 13.5 - - - +
1086C LEU* 2.6 30.2 + - - +
1087C ASP* 3.0 17.7 + - + +
1089C VAL* 3.7 28.5 - - + -
1101C ALA 4.3 0.2 - - - -
1102C LEU* 1.3 70.9 - - - +
1104C ILE* 1.3 70.3 + - - +
1143C TYR* 4.0 25.1 - - + -
1144C LEU 3.5 11.9 - - - +
1145C VAL* 4.4 6.5 - - + +
1162C LEU* 4.4 2.9 - - + -
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Residues in contact with ILE1104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1085C ALA* 4.4 2.2 - - - -
1086C LEU* 4.4 3.4 - - + +
1102C LEU* 3.7 28.5 - - + +
1103C ILE* 1.3 85.7 - - - +
1105C ASP* 1.3 68.5 + - - +
1106C PRO* 3.1 13.5 - - - +
1108C MET* 3.7 25.1 - - - -
1120C ILE* 3.5 26.9 - - + -
1121C PRO 4.2 4.9 - - - +
1123C PRO* 4.1 8.5 - - + -
1144C LEU* 3.0 22.2 + - + +
1146C LEU* 4.0 12.6 - - + +
1154C TRP* 3.8 32.5 - - + -
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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