Contacts of the strand formed by residues 1097 - 1109 (chain F) in PDB entry 1NYE
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 SER1097 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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830E HIS* 3.5 21.2 - - - -
831E TRP 3.4 7.9 - - - -
832E GLU* 4.4 2.0 - - - +
1095F PRO 3.2 1.4 - - - -
1096F THR* 1.3 89.7 + - - +
1098F ILE* 1.3 70.5 + - - +
1099F ASP* 3.5 11.1 + - - -
1123F GLU 4.5 1.6 + - - -
1124F VAL* 3.6 0.7 - - - -
1125F ALA* 2.9 35.2 + - - +
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Residues in contact with ILE1098 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829E ALA 3.8 0.9 - - - +
830E HIS* 3.3 5.4 - - - -
831E TRP* 2.7 41.6 + - + +
1081F SER* 3.8 23.3 + - - +
1084F LEU* 3.4 36.3 - - + -
1085F SER* 4.1 4.7 - - - +
1095F PRO* 3.8 28.0 - - + -
1097F SER* 1.3 81.7 + - - +
1099F ASP* 1.3 61.0 + - - +
1100F THR* 3.4 26.9 - - + -
1122F SER* 4.1 2.5 - - - +
1123F GLU 3.8 3.6 - - - -
1124F VAL* 3.7 13.5 - - + -
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Residues in contact with ASP1099 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828E GLN* 4.4 10.6 - - - +
829E ALA 3.7 4.0 - - - +
830E HIS* 2.4 35.1 + - - +
1097F SER* 3.5 15.8 + - - -
1098F ILE* 1.3 70.6 - - - +
1100F THR* 1.3 61.1 + - - +
1101F THR* 5.2 1.0 + - - -
1121F LYS* 4.0 0.7 + - - +
1122F SER* 3.2 0.9 - - - -
1123F GLU* 2.7 56.1 + - + +
1162F LYS* 5.9 0.9 + - - -
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Residues in contact with THR1100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828E GLN* 3.2 6.2 + - - +
829E ALA 3.0 29.7 + - - -
1077F ALA* 3.5 18.4 + - - +
1080F PHE* 3.8 17.3 - - + -
1081F SER* 2.8 27.2 + - - +
1098F ILE* 3.4 14.8 - - + -
1099F ASP* 1.3 74.6 - - - +
1101F THR* 1.3 64.4 + - - +
1120F LEU* 5.6 2.0 - - - -
1121F LYS 3.3 4.3 - - - -
1122F SER* 2.8 29.4 - - - +
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Residues in contact with THR1101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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826E LYS* 4.9 16.2 - - + +
827E GLY 3.8 10.5 - - - +
828E GLN* 4.0 15.7 + - + +
1077F ALA* 4.7 0.9 - - - -
1099F ASP 5.2 1.0 + - - -
1100F THR* 1.3 76.4 - - - +
1102F ALA* 1.3 69.9 + - - +
1103F ASP* 4.2 1.3 - - + -
1119F ALA 3.5 0.6 - - - +
1120F LEU* 3.3 9.1 - - - +
1121F LYS* 2.5 60.2 + - - -
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Residues in contact with ALA1102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825E LYS 4.0 0.2 - - - +
826E LYS* 3.4 8.0 - - - +
827E GLY 3.0 30.0 + - - +
1073F GLY* 3.3 34.9 - - - +
1076F HIS* 4.6 0.2 - - + -
1077F ALA* 4.0 6.3 - - + +
1100F THR 4.4 0.2 + - - -
1101F THR* 1.3 76.9 - - - +
1103F ASP* 1.3 60.2 + - - +
1104F VAL* 3.9 1.3 + - - -
1118F ILE* 4.4 7.2 - - + -
1119F ALA 3.5 3.8 - - - -
1120F LEU* 3.7 18.4 - - + -
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Residues in contact with ASP1103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824E HIS* 2.9 42.7 + - - +
825E LYS 4.0 4.4 - - - +
826E LYS* 4.1 23.7 + - + +
1101F THR* 4.2 1.5 - - + -
1102F ALA* 1.3 70.5 - - - +
1104F VAL* 1.3 62.6 + - - +
1105F SER* 3.9 1.7 + - - -
1117F LYS 3.5 2.1 - - - +
1118F ILE* 3.0 5.0 - - - -
1119F ALA* 2.7 52.4 + - + +
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Residues in contact with VAL1104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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823E ILE 3.6 1.6 - - - +
824E HIS* 3.5 5.4 - - - -
825E LYS* 2.9 37.9 + - - +
1069F GLU* 3.6 36.8 - - + +
1072F ILE* 4.6 1.3 - - + -
1073F GLY* 3.5 32.1 - - - +
1102F ALA 4.7 1.1 - - - +
1103F ASP* 1.3 73.7 + - - +
1105F SER* 1.3 63.4 + - - +
1106F LEU 3.9 0.5 + - - -
1115F ILE* 3.6 30.7 - - + -
1117F LYS 3.6 2.9 - - - -
1118F ILE* 4.0 17.9 - - + -
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Residues in contact with SER1105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822E THR* 3.8 12.4 + - - -
823E ILE 3.6 4.7 - - - -
824E HIS* 3.0 28.2 + - - -
1103F ASP* 4.9 1.7 + - - -
1104F VAL* 1.3 71.3 - - - +
1106F LEU* 1.3 60.5 + - - +
1107F ASP* 3.8 0.9 - - - -
1115F ILE* 3.3 5.0 - - - -
1116F THR* 2.8 40.3 + - - -
1117F LYS* 2.6 30.9 + - - +
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Residues in contact with LEU1106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821E MET 4.7 1.0 - - - +
822E THR* 4.0 0.2 - - - -
823E ILE* 2.9 58.6 + - + +
946E PRO* 4.1 17.3 - - + -
1059F ARG* 5.4 5.8 - - + +
1069F GLU* 4.1 26.0 - - + +
1104F VAL 3.9 1.0 + - - -
1105F SER* 1.3 69.5 - - - +
1107F ASP* 1.3 59.4 + - - +
1108F LYS 4.3 0.3 + - - -
1113F PHE* 3.7 30.9 - - + -
1114F ALA 3.6 29.8 - - - +
1115F ILE* 3.9 9.0 - - + +
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Residues in contact with ASP1107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822E THR* 2.7 40.7 + - - -
1105F SER* 3.7 1.8 + - - -
1106F LEU* 1.3 72.1 - - - +
1108F LYS* 1.3 73.9 + - + +
1109F VAL* 3.1 10.2 + - + +
1113F PHE* 3.2 6.8 - - - -
1114F ALA 2.9 32.1 + - - -
1116F THR* 2.9 35.9 + - + +
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Residues in contact with LYS1108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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818E GLN 5.1 0.2 - - - +
819E GLY* 3.9 18.3 + - - +
820E HIS* 3.2 40.9 + - - +
821E MET 3.3 20.6 - - - +
822E THR* 4.5 0.4 - - - +
1107F ASP* 1.3 83.8 + - - +
1109F VAL* 1.3 60.7 + - - +
1110F ASP 3.9 4.8 + - - +
1112F GLY 3.4 3.4 - - - +
1113F PHE* 3.3 29.7 - - + -
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Residues in contact with VAL1109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1107F ASP* 3.1 14.9 + - + +
1108F LYS* 1.3 74.6 - - - +
1110F ASP* 1.3 84.5 + - - +
1112F GLY* 2.5 31.2 + - - +
1114F ALA* 4.3 14.4 - - + -
1116F THR* 3.9 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