Contacts of the strand formed by residues 1099 - 1106 (chain D) in PDB entry 4OUL
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 GLN1099 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1036D ARG* 2.3 43.2 + - + -
1037D PHE 3.3 3.4 - - - +
1038D ASN* 3.3 24.4 + - + +
1065D MET 3.6 0.7 - - - +
1066D LYS* 3.4 2.5 - - - +
1067D ASN* 2.7 50.3 + - - +
1097D GLY 4.0 10.1 + - - +
1098D ASP* 1.3 78.0 - - - +
1100D ILE* 1.3 62.4 + - - +
1101D TRP* 3.6 7.1 - - + -
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Residues in contact with ILE1100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035D GLY 4.2 0.3 - - - +
1036D ARG* 3.7 0.5 - - - -
1037D PHE* 2.8 50.4 + - + +
1047D PHE* 3.6 36.6 - - + -
1064D LEU* 3.5 27.6 - - + -
1065D MET 3.3 4.5 - - - +
1066D LYS* 3.9 33.9 - - + -
1071D LEU* 4.3 0.4 - - + -
1092D LEU* 4.1 10.3 - - + -
1094D LEU* 3.7 26.2 - - + -
1098D ASP* 5.4 0.2 - - + -
1099D GLN* 1.3 74.6 - - - +
1101D TRP* 1.3 66.0 + - - +
1119D PHE* 4.2 4.4 - - + -
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Residues in contact with TRP1101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014D ASP 5.5 1.6 - - - -
1015D GLN 4.9 0.2 - - - -
1016D PRO* 4.0 29.4 - - + -
1034D LEU 5.5 0.9 - - - +
1035D GLY 3.4 17.9 - - - +
1036D ARG* 3.9 23.7 - - + +
1064D LEU* 3.7 4.9 - - - +
1065D MET* 2.8 56.3 + - + +
1067D ASN* 2.8 31.3 + - - +
1068D GLU* 4.3 13.0 - - - -
1099D GLN* 3.6 16.1 - - + +
1100D ILE* 1.3 81.2 - - - +
1102D LEU* 1.3 81.5 + - - +
1103D ARG* 3.7 31.4 - - + -
1119D PHE* 4.2 5.2 - - - -
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Residues in contact with LEU1102 (chain D).
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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1017D ILE* 2.8 47.7 + - + +
1019D PHE* 4.2 4.0 - - + -
1035D GLY 4.3 2.8 + - - -
1049D PHE* 3.7 46.2 - - + -
1051D MET* 3.8 20.9 - - + -
1062D VAL* 4.2 4.3 - - + -
1063D ASN 3.4 10.1 - - - +
1064D LEU* 3.6 28.3 - - + -
1101D TRP* 1.3 81.7 - - - +
1103D ARG* 1.3 59.7 + - - +
1119D PHE* 3.7 28.2 - - + -
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Residues in contact with ARG1103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014D ASP* 3.4 52.6 + - - +
1015D GLN 3.8 3.1 - - - +
1017D ILE* 4.2 2.5 - - - -
1062D VAL* 3.3 5.0 - - - +
1063D ASN* 2.8 63.8 + - - +
1065D MET* 3.7 31.8 - - + +
1068D GLU* 5.1 5.5 + - - -
1070D VAL* 3.6 16.5 - - - +
1101D TRP* 3.7 19.0 + - + -
1102D LEU* 1.3 72.7 - - - +
1104D LEU* 1.3 61.6 + - - +
1105D HIS* 3.2 5.7 + - - -
1114F TRP* 3.4 26.1 - - - -
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Residues in contact with LEU1104 (chain D).
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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1008D LEU* 4.1 12.6 - - + +
1010D PRO* 3.5 37.2 - - + -
1012D THR 5.0 1.0 - - - +
1013D LEU* 4.1 0.9 - - - -
1014D ASP* 3.0 17.5 + - - -
1015D GLN* 2.9 22.1 + - - +
1016D PRO 5.4 0.2 - - - -
1017D ILE* 3.7 18.2 - - + +
1060D LEU* 3.4 22.0 - - + -
1061D TYR 3.9 3.1 - - - +
1062D VAL* 4.6 1.1 - - + +
1103D ARG* 1.3 69.0 - - - +
1105D HIS* 1.3 63.3 + - - +
1106D ARG* 3.2 30.7 - - - +
1107D GLY 3.7 10.5 - - - +
1109D ILE* 4.1 17.9 - - + -
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Residues in contact with HIS1105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013D LEU* 3.3 27.1 - - + +
1014D ASP* 2.5 56.4 + - - +
1061D TYR* 2.9 31.3 + + + +
1063D ASN* 3.6 17.0 - - - +
1103D ARG* 3.2 6.6 + - - -
1104D LEU* 1.3 71.9 - - - +
1106D ARG* 1.3 87.0 + - + +
1114F TRP* 3.7 30.6 - + + -
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Residues in contact with ARG1106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013D LEU* 4.8 21.9 - - + +
1058D VAL* 4.1 11.2 - - + -
1059D PRO* 3.4 28.5 - - - +
1060D LEU* 3.4 1.2 - - - -
1061D TYR* 3.0 58.5 + - + -
1104D LEU* 3.2 14.2 - - - +
1105D HIS* 1.3 106.3 + - + +
1107D GLY* 1.3 65.7 + - - +
1202D GOL 5.9 2.6 - - - -
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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