Contacts of the strand formed by residues 1115 - 1119 (chain B) in PDB entry 5FLM
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 GLN1115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A SER* 5.0 4.1 + - - -
80A GLU* 4.7 25.8 - - - +
1114B TYR* 1.3 106.1 + - - +
1116B VAL* 1.3 63.1 + - - +
1117B HIS* 5.8 0.6 - - - -
1148B LEU* 3.7 33.6 - - + +
1149B VAL 3.4 4.0 - - - -
1150B ARG* 3.1 46.8 - - + +
1151B MET* 4.8 0.4 - - - +
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Residues in contact with VAL1116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO* 4.9 4.7 - - + -
1114B TYR* 3.3 30.7 - - + +
1115B GLN* 1.3 71.2 - - - +
1117B HIS* 1.3 61.4 + - - +
1118B VAL* 3.7 19.6 + - + -
1125B MET* 3.8 20.9 - - + -
1148B LEU* 3.7 4.7 - - - +
1149B VAL* 2.9 40.7 + - + +
1151B MET* 3.6 24.0 - - - +
1156B LYS* 3.6 18.8 - - + -
1171B MET* 4.5 2.9 - - + -
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Residues in contact with HIS1117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A SER* 4.3 13.6 - - - -
13A CYS* 3.4 34.6 - - + +
80A GLU* 4.4 14.8 + - - -
1115B GLN* 5.8 0.6 - - - -
1116B VAL* 1.3 73.6 - - - +
1118B VAL* 1.3 59.9 + - - +
1125B MET* 3.4 6.9 - - - +
1126B ALA* 2.8 32.7 + - + +
1127B ILE 5.4 0.2 - - - +
1128B ALA* 3.4 32.4 - - + +
1130B THR* 5.0 4.7 - - - -
1135B TYR* 3.9 24.4 + + + -
1146B ILE* 3.7 13.9 - - + -
1147B SER 3.6 2.2 - - - -
1148B LEU* 3.9 22.2 - - + +
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Residues in contact with VAL1118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116B VAL* 3.7 19.1 - - + +
1117B HIS* 1.3 78.3 - - - +
1119B CYS* 1.3 76.1 + - - +
1120B ASN* 4.1 0.2 - - - +
1123B GLY 3.7 16.6 - - - +
1124B ILE 3.4 14.6 - - - +
1125B MET* 4.5 8.1 - - + -
1146B ILE* 3.8 3.4 - - - -
1147B SER* 2.9 36.2 + - - +
1149B VAL* 4.3 10.5 - - + -
1171B MET* 3.5 40.8 - - + +
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Residues in contact with CYS1119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117B HIS 4.4 0.4 + - - -
1118B VAL* 1.3 85.0 - - - +
1120B ASN* 1.3 69.5 + - - +
1121B LEU* 3.5 9.4 - - - -
1122B CYS* 2.7 24.9 - - - +
1124B ILE 3.2 8.9 + - - +
1126B ALA* 4.4 3.0 - - + +
1137B CYS* 3.5 19.3 - - + -
1142B ASN* 3.3 27.1 - - - -
1145B GLN 4.1 0.7 - - - -
1146B ILE* 4.2 10.8 - - + +
1171B MET 4.1 3.6 - - - +
2175B ZN 2.6 35.9 - - - -
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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