Contacts of the strand formed by residues 999 - 1008 (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 ILE 999 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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994G VAL* 3.9 25.1 - - + -
995G ALA 4.4 0.7 - - - +
996G ARG 2.9 21.2 + - - +
997G GLU 3.2 4.2 - - - +
998G LYS* 1.3 81.5 - - - +
1000G THR* 1.3 70.4 + - - +
1001G MET* 4.7 3.1 - - + -
1017G VAL 3.7 2.9 - - - +
1018G ALA* 3.3 34.5 - - + -
1021G VAL* 4.7 1.3 - - + -
1032G ILE* 3.8 26.9 - - + -
1069G VAL* 4.1 5.6 - - + -
1076G LEU* 4.1 20.2 - - + -
1078G ILE* 3.6 25.1 - - + -
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Residues in contact with THR1000 (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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997G GLU 5.3 2.2 - - - +
998G LYS 4.4 5.6 - - - +
999G ILE* 1.3 82.8 - - - +
1001G MET* 1.3 69.4 + - - +
1002G SER* 3.9 5.2 + - - -
1016G GLY* 3.5 2.4 - - - -
1017G VAL* 3.2 44.7 + - + +
1019G LYS* 5.5 8.5 - - + -
1032G ILE* 5.7 0.2 - - - -
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Residues in contact with MET1001 (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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999G ILE* 4.7 5.2 - - + -
1000G THR* 1.3 81.0 + - - +
1002G SER* 1.3 61.3 + - - +
1014G TYR* 3.7 55.0 - - + -
1015G GLU 3.9 4.0 - - - -
1016G GLY* 4.5 0.4 - - - -
1032G ILE* 4.0 23.6 - - + -
1034G THR* 3.8 17.9 - - + -
1076G LEU* 4.5 7.4 - - + -
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Residues in contact with SER1002 (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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1000G THR* 4.2 5.5 + - - -
1001G MET* 1.3 78.1 - - - +
1003G ARG* 1.3 67.5 + - - +
1014G TYR* 5.7 1.1 - - - -
1015G GLU* 2.9 20.0 + - - -
1016G GLY* 3.9 10.8 - - - -
1017G VAL* 4.8 7.4 - - - +
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Residues in contact with ARG1003 (chain G).
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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7G 741 4.4 20.0 - - - +
1002G SER* 1.3 86.7 - - - +
1004G GLU* 1.3 75.8 + - - +
1005G LEU* 3.9 20.9 - - - +
1014G TYR* 4.2 5.8 - - - +
1015G GLU* 2.8 52.0 + - + +
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Residues in contact with GLU1004 (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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1003G ARG* 1.3 90.1 + - - +
1005G LEU* 1.3 64.6 + - - +
1006G GLY* 4.7 1.7 - - - +
1012G MET* 3.5 31.9 - - - +
1013G VAL 3.7 5.4 - - - -
1014G TYR* 3.5 30.9 + - + -
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Residues in contact with LEU1005 (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 3.5 71.8 - - + +
1003G ARG* 3.9 22.0 - - - +
1004G GLU* 1.3 82.4 - - - +
1006G GLY* 1.3 56.3 + - - +
1013G VAL* 2.7 22.1 + - + +
1014G TYR 4.0 10.1 - - - +
1015G GLU* 3.8 35.2 - - + +
1031G ALA* 4.7 1.3 - - + -
1081G LEU* 4.3 8.3 - - + -
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Residues in contact with GLY1006 (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 4.6 3.8 + - - -
1004G GLU* 4.7 0.9 - - - +
1005G LEU* 1.3 80.8 - - - +
1007G GLN* 1.3 62.9 + - - -
1012G MET* 3.2 13.7 - - - +
1013G VAL* 2.9 29.7 + - - +
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Residues in contact with GLN1007 (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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1006G GLY* 1.3 74.1 - - - -
1008G GLY* 1.3 66.7 + - - +
1010G PHE 5.4 0.2 - - - -
1011G GLY* 3.5 26.6 + - - +
1012G MET* 3.4 25.3 - - + +
1013G VAL* 4.5 2.0 - - - +
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Residues in contact with GLY1008 (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 6.1 0.4 - - - -
1006G GLY 3.8 1.2 + - - -
1007G GLN* 1.3 85.6 + - - +
1009G SER* 1.3 70.5 + - - +
1010G PHE 3.0 3.0 + - - -
1011G GLY* 2.6 28.7 + - - +
1013G VAL* 4.0 8.3 - - - +
1033G LYS* 3.6 12.8 - - - -
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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