Contacts of the strand formed by residues 1075 - 1080 (chain T) in PDB entry 3F5P
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 THR1075 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982T SER* 5.1 1.2 + - - -
984T ALA* 3.4 29.5 - - + +
996T ARG* 4.4 0.4 - - - +
1033T LYS 3.3 3.6 - - - +
1034T THR* 3.5 1.2 - - - -
1035T VAL* 3.0 43.6 + - - +
1044T ARG* 4.2 13.4 + - - +
1047T PHE* 4.4 17.0 - - + -
1048T LEU* 4.7 7.4 - - + -
1068T VAL* 4.5 7.9 - - + -
1069T VAL 3.6 14.5 + - - +
1070T SER* 4.6 4.0 + - - +
1072T GLY 5.0 3.6 + - - -
1073T GLN 3.8 2.7 + - - -
1074T PRO* 1.3 71.8 - - - +
1076T LEU* 1.3 69.6 + - - +
1077T VAL* 4.7 0.4 - - + -
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Residues in contact with LEU1076 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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996T ARG* 4.0 12.6 - - + +
999T ILE* 3.9 28.0 - - + +
1001T MET* 4.6 7.6 - - - -
1032T ILE* 4.0 13.5 - - + -
1033T LYS 3.2 2.2 - - - +
1034T THR* 3.6 29.2 - - + -
1068T VAL* 3.2 11.3 - - - +
1069T VAL* 2.9 55.4 + - + -
1074T PRO* 3.6 20.4 - - + +
1075T THR* 1.3 81.8 - - - +
1077T VAL* 1.3 63.4 + - - +
1078T ILE* 4.1 2.0 - - + -
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Residues in contact with VAL1077 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T 741 3.0 35.5 - - - +
1032T ILE* 3.5 1.7 - - - -
1033T LYS* 3.0 30.9 + - + -
1047T PHE* 3.0 41.5 - - + -
1048T LEU* 5.7 2.0 - - + -
1051T ALA* 4.9 9.0 - - + -
1065T LEU* 3.9 28.7 - - + -
1067T GLY 3.9 4.3 - - - +
1068T VAL* 4.3 10.3 - - + -
1075T THR* 4.7 2.5 - - + -
1076T LEU* 1.3 77.9 - - - +
1078T ILE* 1.3 62.9 + - - +
1079T MET* 4.6 2.5 - - + -
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Residues in contact with ILE1078 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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994T VAL* 4.4 3.6 - - + -
999T ILE* 3.9 22.7 - - + -
1018T ALA* 4.5 5.2 - - + -
1021T VAL* 5.2 2.0 - - + -
1030T VAL* 3.7 27.4 - - + -
1031T ALA 3.5 2.9 - - - -
1032T ILE* 3.7 22.0 - - + -
1065T LEU* 3.7 4.2 - - - +
1066T LEU* 2.7 52.7 + - + -
1067T GLY* 2.8 31.2 + - - +
1069T VAL* 4.2 20.6 - - + -
1076T LEU* 4.2 11.7 - - + +
1077T VAL* 1.3 73.5 - - - +
1079T MET* 1.3 57.5 + - - +
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Residues in contact with MET1079 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T 741 3.2 84.1 - - + +
1030T VAL* 3.4 7.4 - - - +
1031T ALA 2.9 27.1 + - - +
1054T MET* 3.2 27.1 - - + -
1063T VAL* 3.8 24.0 - - + +
1064T ARG 3.6 1.8 - - - +
1065T LEU* 3.6 28.5 - - - -
1066T LEU* 4.5 1.3 - - - -
1077T VAL* 3.7 2.6 + - + -
1078T ILE* 1.3 77.7 - - - +
1080T GLU* 1.3 65.3 + - - +
1081T LEU 3.3 0.3 + - - -
1152T GLY 5.0 2.5 - - - +
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Residues in contact with GLU1080 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16T 741 3.5 12.3 - - - -
1029T ARG 5.1 0.2 - - - -
1030T VAL* 5.1 0.2 - - - +
1031T ALA 4.5 0.2 - - - -
1062T VAL 4.0 1.6 - - - +
1063T VAL* 3.5 15.1 - - + +
1064T ARG* 2.9 48.5 + - + +
1066T LEU* 4.2 19.3 - - + +
1079T MET* 1.3 73.2 - - - +
1081T LEU* 1.3 71.1 + - - +
1082T MET* 3.5 11.8 + - - +
1144T ALA* 5.7 0.5 - - - +
1150T LYS* 2.6 35.7 + - - +
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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