Contacts of the strand formed by residues 1025 - 1034 (chain E) 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 GLU1025 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020E GLY* 3.6 14.4 + - - -
1021E VAL 4.4 0.3 + - - -
1022E VAL* 2.8 35.3 + - + +
1023E LYS 4.7 1.7 - - - +
1024E ASP* 1.3 83.4 - - - +
1026E PRO* 1.3 69.6 - - + +
1027E GLU* 2.8 20.7 - - - +
1028E THR* 3.3 26.5 + - - +
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Residues in contact with PRO1026 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019E LYS* 3.2 12.2 - - - +
1020E GLY* 2.8 26.2 + - - +
1024E ASP 3.5 9.9 - - - +
1025E GLU* 1.3 87.1 - - + +
1027E GLU* 1.3 65.1 + - + +
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Residues in contact with GLU1027 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017E VAL* 3.9 20.5 - - + +
1018E ALA 3.7 4.7 - - - -
1019E LYS* 3.9 27.0 + - + +
1025E GLU* 2.8 25.3 - - - +
1026E PRO* 1.3 89.6 - - + +
1028E THR* 1.3 61.4 + - - +
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Residues in contact with THR1028 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017E VAL* 3.3 8.2 - - - -
1018E ALA 2.8 41.7 + - - -
1021E VAL* 4.0 4.6 - - - +
1022E VAL* 2.9 41.8 + - + +
1025E GLU* 3.3 16.0 + - - +
1027E GLU* 1.3 79.2 + - - +
1029E ARG* 1.3 78.5 + - - +
1030E VAL* 3.9 5.5 - - + +
1066E LEU* 4.8 3.4 - - + -
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Residues in contact with ARG1029 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015E GLU* 2.2 35.0 + - - +
1016E GLY 3.6 8.0 + - - +
1017E VAL* 4.8 5.8 - - + +
1028E THR* 1.3 84.4 - - - +
1030E VAL* 1.3 65.2 + - - +
1080E GLU* 4.8 0.7 - - - -
1081E LEU* 3.5 36.0 + - + +
1083E THR* 4.0 11.8 - - - +
1145E GLU* 3.8 20.4 + - - -
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Residues in contact with VAL1030 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015E GLU* 3.8 2.4 - - - -
1016E GLY 3.0 35.7 + - - +
1018E ALA* 3.6 35.4 - - + +
1028E THR* 3.9 5.8 - - + +
1029E ARG* 1.3 81.4 - - - +
1031E ALA* 1.3 61.0 + - - +
1032E ILE* 3.1 29.6 + - + -
1066E LEU* 3.4 30.5 - - + -
1078E ILE* 3.8 7.2 - - + -
1079E MET 3.4 9.0 - - - +
1081E LEU* 3.7 11.8 - - - +
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Residues in contact with ALA1031 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E 741 3.6 53.8 - - + +
1005E LEU* 4.6 2.0 - - + -
1013E VAL* 4.2 3.6 - - + -
1014E TYR 3.4 9.0 - - - +
1030E VAL* 1.3 73.9 - - - +
1032E ILE* 1.3 62.3 - - - +
1078E ILE* 3.5 4.2 - - - -
1079E MET 2.8 34.0 + - - +
1081E LEU* 4.0 7.9 - - + +
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Residues in contact with ILE1032 (chain E).
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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5E 741 4.0 1.6 - - - -
999E ILE* 3.4 22.4 - - + -
1001E MET* 4.1 23.1 - - + -
1012E MET 3.7 1.2 - - - +
1013E VAL* 3.4 2.4 - - - -
1014E TYR* 2.7 45.3 + - - +
1016E GLY* 4.7 8.3 - - - +
1030E VAL* 3.1 37.2 - - + +
1031E ALA* 1.3 75.8 - - - +
1033E LYS* 1.3 61.2 + - - +
1034E THR* 5.0 0.2 - - - +
1076E LEU* 3.7 33.9 - - + -
1077E VAL 3.3 11.7 - - - +
1078E ILE* 3.9 13.9 - - + -
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Residues in contact with LYS1033 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E 741 2.9 54.8 + - + +
1008E GLY* 3.0 3.8 - - - -
1009E SER* 2.7 47.1 + - - +
1010E PHE 3.1 6.5 - - - +
1011E GLY* 3.9 13.7 - - - +
1012E MET 3.7 5.6 - - - +
1013E VAL* 3.8 20.6 - - + +
1032E ILE* 1.3 73.6 - - - +
1034E THR* 1.3 72.6 + - - +
1035E VAL* 5.2 0.7 - - + -
1047E PHE* 3.7 17.0 - - + -
1075E THR 3.4 5.5 - - - +
1076E LEU* 3.5 4.9 - - - +
1077E VAL* 2.9 36.7 + - + +
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Residues in contact with THR1034 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001E MET* 4.1 24.5 - - + -
1011E GLY* 3.5 7.6 - - - -
1012E MET* 3.1 42.9 + - - +
1014E TYR* 4.1 6.0 - - + -
1032E ILE 5.0 0.9 - - - +
1033E LYS* 1.3 75.3 - - - +
1035E VAL* 1.3 63.2 + - - +
1036E ASN* 3.8 3.2 + - - +
1074E PRO* 4.5 15.5 - - + -
1075E THR 3.6 2.5 - - - -
1076E LEU* 3.5 26.0 - - + -
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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