Contacts of the strand formed by residues 1118 - 1126 (chain E) 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 THR1118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1001E SER* 5.5 2.5 - - - +
1002E ALA 3.1 11.4 - - - +
1003E ALA* 4.3 7.0 - - + -
1019E PHE* 4.4 0.4 - - - -
1023E LEU* 5.2 2.0 - - + -
1049E PHE* 3.3 1.7 - - - -
1050E HIS* 2.8 33.7 + - - +
1051E MET* 3.2 10.6 - - - +
1115E LYS 3.8 10.8 - - - +
1117E SER* 1.3 79.7 - - - +
1119E PHE* 1.3 61.3 + - - +
1120E SER* 5.3 0.7 - - - -
1072F VAL* 3.7 26.7 - - + -
1088F ASN* 2.6 29.6 + - - +
1089F HIS* 3.0 20.0 - - - +
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Residues in contact with PHE1119 (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 PHE* 3.7 17.0 - + - -
1001E SER* 3.5 0.9 - - - -
1002E ALA* 2.8 32.7 + - + +
1019E PHE* 3.4 37.2 - + + -
1030E PHE* 3.9 25.8 - + - -
1035E GLY 4.6 1.1 - - - -
1047E PHE* 4.3 7.2 - - + -
1048E ILE 3.5 11.7 - - - -
1049E PHE* 3.9 8.7 - + + -
1064E LEU* 3.9 30.3 - - + -
1100E ILE* 4.1 13.5 - - + -
1101E TRP* 4.3 5.4 - - - -
1102E LEU* 3.8 25.8 - - + -
1118E THR* 1.3 77.5 - - - +
1120E SER* 1.3 75.8 + - - +
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Residues in contact with SER1120 (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 PHE* 3.2 20.6 - - - -
1001E SER* 2.5 26.7 + - - -
1047E PHE* 3.2 5.9 - - - +
1048E ILE* 2.9 33.4 + - - +
1119E PHE* 1.3 75.6 - - - +
1121E GLY* 1.3 59.2 + - - +
1089F HIS* 2.7 32.1 + - - -
1091F ILE* 3.6 15.2 - - - +
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Residues in contact with GLY1121 (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 VAL* 6.0 0.2 - - - -
999E ALA* 3.3 1.0 - - - +
1000E PHE* 2.9 50.5 + - - +
1037E PHE* 6.2 0.2 - - - -
1046E VAL 2.9 14.6 - - - -
1047E PHE* 3.7 5.2 - - - -
1120E SER* 1.3 78.6 - - - +
1122E TYR* 1.3 68.7 + - - +
1091F ILE* 4.1 1.1 - - - +
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Residues in contact with TYR1122 (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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1122D TYR* 2.3 40.1 + + - -
998E VAL* 3.1 15.9 - - - +
999E ALA* 3.7 5.4 - - + +
1045E TYR* 3.4 12.3 - - - -
1046E VAL* 3.0 58.5 + - + +
1047E PHE* 5.1 0.2 - - - -
1048E ILE* 5.4 4.0 - - + -
1121E GLY* 1.3 76.0 - - - +
1123E LEU* 1.3 67.7 + - - +
1124E LEU* 4.1 18.6 - - + -
1046F VAL* 4.2 11.9 - - + -
1091F ILE* 3.6 20.4 - - + -
1122F TYR* 2.4 13.3 + + - -
1124F LEU* 3.5 41.3 - - + -
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Residues in contact with LEU1123 (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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997E ARG* 3.7 36.7 + - + +
998E VAL* 2.8 20.5 + - + -
1041E VAL* 5.5 4.3 - - + -
1043E GLY* 4.2 2.2 - - - -
1044E THR 3.2 18.6 - - - +
1045E TYR* 3.5 41.5 - - + +
1122E TYR* 1.3 78.1 - - - +
1124E LEU* 1.3 60.3 + - - +
1125E TYR 3.2 23.6 - - - +
1126E GLN* 4.0 19.3 - - + +
1124F LEU* 4.5 1.9 - - - +
1125F TYR* 2.8 31.3 + - - +
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Residues in contact with LEU1124 (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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999D ALA* 4.0 9.6 - - + -
1122D TYR* 3.5 50.5 - - + -
1123D LEU 4.9 1.6 - - - +
1124D LEU* 5.9 1.1 - - + -
997E ARG* 4.8 6.4 + - - -
1044E THR* 2.8 25.6 + - + +
1046E VAL* 4.1 17.5 - - + -
1091E ILE* 4.5 1.1 - - + -
1122E TYR* 3.5 15.7 + - + +
1123E LEU* 1.3 75.7 - - - +
1125E TYR* 1.3 99.1 + - + +
1126E GLN 4.4 0.2 - - - -
1124F LEU* 5.6 3.1 - - + -
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Residues in contact with TYR1125 (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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996D MET* 3.6 40.4 - - + +
997D ARG* 3.6 8.8 - - + +
998D VAL 3.1 46.5 + - - -
999D ALA* 4.4 0.7 - - + -
1026D LEU* 3.3 26.0 - - + -
1123D LEU* 3.2 21.7 + - - +
997E ARG* 5.1 1.3 - - - +
1043E GLY* 3.1 3.6 - - - -
1044E THR* 2.7 38.2 + - - +
1123E LEU* 3.2 4.9 - - - +
1124E LEU* 1.3 112.8 - - + +
1126E GLN* 1.3 60.8 + - - +
1127E ASP 4.6 1.2 - - - -
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Residues in contact with GLN1126 (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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996D MET* 3.1 21.8 - - - +
997E ARG* 3.9 45.1 + - - +
1041E VAL* 3.5 34.7 - - + +
1042E ASN 3.7 2.9 - - - +
1123E LEU* 4.0 12.0 - - + +
1125E TYR* 1.3 74.2 - - - +
1127E ASP* 1.3 85.3 + - - +
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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