Contacts of the strand formed by residues 1025 - 1035 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1020G GLY* 3.8 14.6 + - - -
1021G VAL 4.3 1.4 + - - -
1022G VAL* 2.8 33.6 + - + +
1023G LYS 4.5 1.1 - - - +
1024G ASP* 1.3 83.7 - - - +
1026G PRO* 1.3 68.4 - - + +
1027G GLU* 2.8 15.1 + - - +
1028G THR* 2.4 42.0 + - - +
998S LYS* 4.2 6.8 - - - +
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Residues in contact with PRO1026 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019G LYS* 3.4 7.4 - - - +
1020G GLY 3.0 19.8 + - - +
1024G ASP 4.1 1.6 - - - +
1025G GLU* 1.3 86.6 - - + +
1027G GLU* 1.3 68.0 + - + +
997S GLU* 3.9 38.1 - - + +
998S LYS* 4.2 11.4 - - + -
1019S LYS* 3.3 37.3 - - + +
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Residues in contact with GLU1027 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017G VAL* 3.5 22.9 - - + +
1018G ALA 3.6 6.5 - - - -
1019G LYS* 3.7 18.6 + - + +
1025G GLU* 2.8 21.7 - - - +
1026G PRO* 1.3 84.8 - - + +
1028G THR* 1.3 64.5 + - - +
1019S LYS* 2.4 34.6 + - - +
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Residues in contact with THR1028 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017G VAL* 3.1 10.2 - - - +
1018G ALA 2.9 37.2 + - - -
1021G VAL* 4.5 1.1 - - - -
1022G VAL* 3.2 34.0 + - + +
1025G GLU* 2.4 28.4 + - - +
1027G GLU* 1.3 75.3 - - - +
1029G ARG* 1.3 78.2 + - - +
1030G VAL* 3.9 11.0 - - + -
1066G LEU* 4.8 2.7 - - + -
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Residues in contact with ARG1029 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015G GLU* 2.4 38.2 + - - -
1016G GLY 3.3 7.9 - - - +
1017G VAL* 4.6 7.2 - - + +
1028G THR* 1.3 83.2 - - - +
1030G VAL* 1.3 64.5 + - - +
1081G LEU* 3.4 36.3 + - + +
1083G THR* 3.7 21.5 - - - +
1145G GLU* 4.1 11.3 + - - -
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Residues in contact with VAL1030 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015G GLU* 3.7 2.6 - - - -
1016G GLY 2.8 42.1 + - - +
1017G VAL 4.2 0.7 - - - -
1018G ALA* 3.8 33.9 - - + +
1028G THR* 3.9 8.1 - - + +
1029G ARG* 1.3 81.2 - - - +
1031G ALA* 1.3 58.5 + - - +
1032G ILE* 3.2 27.8 - - + -
1066G LEU* 3.5 28.5 - - + -
1078G ILE* 3.8 6.1 - - + -
1079G MET 3.5 9.4 - - - +
1081G LEU* 3.7 10.6 - - - +
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Residues in contact with ALA1031 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G 741 3.7 50.9 - - + +
1005G LEU* 4.7 0.9 - - + -
1013G VAL* 4.3 3.6 - - + -
1014G TYR 3.3 8.3 - - - +
1015G GLU* 4.8 0.2 - - - +
1030G VAL* 1.3 73.0 - - - +
1032G ILE* 1.3 66.5 + - - +
1077G VAL 3.6 0.7 - - - +
1079G MET* 2.8 36.8 + - + +
1081G LEU* 3.9 8.9 - - + +
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Residues in contact with ILE1032 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G 741 3.7 1.3 - - - -
999G ILE* 3.8 16.6 - - + -
1001G MET* 4.0 23.3 - - + -
1012G MET 3.6 1.2 - - - +
1013G VAL* 3.2 2.7 - - - -
1014G TYR* 2.5 49.0 + - + +
1016G GLY* 4.8 7.0 - - - +
1030G VAL* 3.2 35.7 - - + +
1031G ALA* 1.3 77.6 - - - +
1033G LYS* 1.3 72.1 + - - +
1076G LEU* 3.9 29.4 - - + -
1077G VAL 3.4 4.7 - - - +
1078G ILE* 3.4 20.2 - - + -
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Residues in contact with LYS1033 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G 741 2.6 64.5 + - + +
1008G GLY* 3.8 23.1 - - - -
1009G SER* 2.8 28.7 + - - +
1010G PHE* 3.6 6.4 - - + +
1011G GLY 4.1 9.4 - - - +
1012G MET 3.4 8.3 - - - +
1013G VAL* 4.1 8.7 - - + +
1032G ILE* 1.3 74.5 - - - +
1034G THR* 1.3 74.0 + - - +
1035G VAL* 4.7 0.7 - - + +
1047G PHE* 3.8 17.7 - - + -
1075G THR 3.6 0.7 - - - +
1076G LEU* 3.4 8.7 - - - +
1077G VAL* 3.1 31.6 + - + +
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Residues in contact with THR1034 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001G MET* 3.8 16.8 - - + -
1011G GLY* 3.5 7.4 - - - -
1012G MET* 3.0 31.8 + - - +
1014G TYR* 3.5 26.9 + - + -
1033G LYS* 1.3 76.7 - - - +
1035G VAL* 1.3 62.7 + - - +
1036G ASN* 3.7 3.4 + - - +
1074G PRO* 4.4 13.0 - - + -
1075G THR 3.5 3.6 - - - -
1076G LEU* 3.2 25.6 - - + -
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Residues in contact with VAL1035 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1010G PHE* 4.0 21.3 - - + +
1033G LYS* 4.8 4.0 - - + -
1034G THR* 1.3 72.4 - - - +
1036G ASN* 1.3 67.1 + - - +
1039G ALA* 4.0 19.7 - - + -
1043G GLU* 6.1 0.7 - - + -
1044G ARG* 4.0 23.1 + - + +
1047G PHE* 3.0 43.3 - - + -
1074G PRO* 3.5 6.0 - - - +
1075G THR* 3.1 42.0 + - - +
1077G VAL* 5.0 0.9 - - + -
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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