Contacts of the strand formed by residues 1011 - 1022 (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 GLY1011 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1007E GLN* 3.7 10.5 + - - -
1008E GLY* 2.5 43.9 + - - +
1010E PHE* 1.3 81.1 - - - +
1012E MET* 1.3 55.2 + - - -
1033E LYS* 4.0 8.3 - - - +
1034E THR 3.5 12.6 - - - -
1036E ASN* 4.6 5.8 - - - -
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Residues in contact with MET1012 (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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1004E GLU* 3.6 31.9 - - - +
1006E GLY* 3.3 24.9 - - - +
1007E GLN* 2.8 33.7 - - - +
1011E GLY* 1.3 72.5 - - - -
1013E VAL* 1.3 67.1 + - - +
1014E TYR* 2.9 33.2 - - + +
1033E LYS* 3.7 0.8 - - - -
1034E THR* 3.1 40.5 + - - +
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Residues in contact with VAL1013 (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 3.8 45.5 - - + +
1004E GLU* 3.7 1.4 - - - -
1005E LEU* 2.8 41.2 + - + -
1006E GLY 3.0 19.2 + - - +
1007E GLN 4.2 3.6 - - - +
1008E GLY* 4.0 11.9 - - - -
1012E MET* 1.3 73.4 - - - +
1014E TYR* 1.3 76.8 + - - +
1031E ALA* 4.2 2.7 - - + -
1032E ILE 3.4 7.2 - - - +
1033E LYS* 3.8 23.1 - - + +
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Residues in contact with TYR1014 (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* 3.3 55.1 - - + +
1002E SER 5.1 1.8 - - - -
1003E ARG* 3.5 19.5 - - - +
1004E GLU* 3.3 30.1 + - + -
1005E LEU* 3.4 14.6 - - - +
1012E MET* 2.9 34.7 - - + +
1013E VAL* 1.3 78.2 - - - +
1015E GLU* 1.3 62.0 + - - +
1031E ALA* 3.4 0.9 - - - -
1032E ILE* 2.7 36.7 + - + +
1034E THR* 4.1 8.3 - - + -
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Residues in contact with GLU1015 (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* 3.7 2.7 - - - -
1002E SER* 2.7 32.6 + - - +
1003E ARG* 2.8 50.0 + - + +
1005E LEU* 3.4 23.0 - - + +
1014E TYR* 1.3 75.1 - - - +
1016E GLY* 1.3 65.1 + - - +
1029E ARG* 2.2 38.0 + - - +
1030E VAL 3.8 7.0 - - - +
1032E ILE* 4.8 1.6 - - - -
1081E LEU* 3.9 13.9 - - + +
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Residues in contact with GLY1016 (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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1000E THR 3.3 12.6 - - - -
1001E MET* 4.3 0.9 - - - -
1002E SER* 4.1 8.3 - - - -
1015E GLU* 1.3 84.6 - - - +
1017E VAL* 1.3 65.9 + - - +
1029E ARG* 3.6 7.3 + - - +
1030E VAL* 3.0 33.2 + - - -
1032E ILE* 4.7 3.8 - - - +
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Residues in contact with VAL1017 (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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998E LYS 3.7 0.7 - - - +
999E ILE* 3.6 2.8 - - - +
1000E THR* 3.0 48.3 + - + +
1002E SER* 6.3 1.3 - - - -
1016E GLY* 1.3 79.7 - - - +
1018E ALA* 1.3 65.3 + - - +
1019E LYS* 4.0 3.8 - - + +
1027E GLU* 3.9 41.1 - - + +
1028E THR 3.3 11.9 - - - +
1029E ARG* 5.3 4.9 - - + -
1030E VAL* 4.1 3.1 - - - +
1032E ILE* 5.1 0.4 - - - +
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Residues in contact with ALA1018 (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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999E ILE* 3.5 16.4 - - + -
1017E VAL* 1.3 72.5 - - - +
1019E LYS* 1.3 64.9 + - - +
1020E GLY 3.5 1.7 + - - -
1021E VAL* 3.4 37.0 - - + +
1028E THR 2.8 30.7 + - - -
1030E VAL* 3.6 23.1 - - + +
1078E ILE* 4.3 2.7 - - + -
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Residues in contact with LYS1019 (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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997E GLU 5.9 0.2 - - - +
998E LYS* 3.0 58.8 + - + +
1000E THR* 5.4 7.0 - - + -
1017E VAL* 4.8 4.9 - - + +
1018E ALA* 1.3 71.5 - - - +
1020E GLY* 1.3 61.9 + - - +
1021E VAL* 3.3 4.5 + - - +
1026E PRO* 3.2 10.3 - - - +
1027E GLU* 3.9 28.8 + - + +
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Residues in contact with GLY1020 (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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998E LYS* 4.7 14.0 + - - -
1018E ALA 3.5 1.4 + - - -
1019E LYS* 1.3 71.0 - - - +
1021E VAL* 1.3 61.8 + - - +
1022E VAL 3.4 5.1 - - - +
1025E GLU 3.6 12.5 + - - -
1026E PRO* 2.8 16.8 + - - -
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Residues in contact with VAL1021 (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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994E VAL* 4.6 18.2 - - + -
998E LYS* 5.6 0.4 - - + -
999E ILE* 4.3 9.9 - - + -
1018E ALA* 3.4 42.4 - - + +
1019E LYS 3.8 9.0 - - - +
1020E GLY* 1.3 79.2 - - - +
1022E VAL* 1.3 79.8 + - + +
1023E LYS* 4.0 9.2 + - - -
1025E GLU 4.4 0.4 + - - -
1028E THR* 4.0 3.8 - - - -
1066E LEU* 4.4 29.5 - - + +
1078E ILE* 5.1 4.3 - - + -
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Residues in contact with VAL1022 (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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1020E GLY 4.5 3.1 - - - +
1021E VAL* 1.3 91.5 - - + +
1023E LYS* 1.3 74.4 + - + +
1024E ASP 3.1 0.7 + - - -
1025E GLU* 2.8 52.6 + - + +
1028E THR* 2.9 39.2 + - + +
1064E ARG* 5.7 5.2 - - - +
1066E LEU* 4.4 17.3 - - + -
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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