Contacts of the strand formed by residues 1106 - 1111 (chain A) in PDB entry 3U9Y
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 SER1106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1025A ASN* 4.7 5.8 - - - +
1103A LEU* 4.2 9.2 - - - -
1104A GLY 3.4 5.1 + - - -
1105A LYS* 1.3 81.6 + - - +
1107A PHE* 1.3 60.8 + - - +
1108A LEU* 3.4 5.7 + - - +
1122A HIS* 3.9 4.7 - - - -
1124A SER* 3.0 23.2 + - - -
1125A VAL 3.3 1.2 - - - -
1126A THR* 2.7 39.5 + - - -
1139A TYR* 4.6 1.7 - - - -
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Residues in contact with PHE1107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106A SER* 1.3 71.1 - - - +
1108A LEU* 1.3 76.5 + - - +
1109A GLN* 3.3 30.1 + - + -
1119A PRO* 4.0 25.6 - - + -
1122A HIS* 3.4 38.9 - + + -
1124A SER 2.8 15.9 + - - +
1125A VAL* 3.5 9.6 - - + +
1126A THR* 2.8 25.4 + - - +
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Residues in contact with LEU1108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106A SER 3.4 5.1 + - - +
1107A PHE* 1.3 85.8 - - - +
1109A GLN* 1.3 59.5 + - - +
1110A PHE* 3.8 35.0 + - + -
1126A THR* 3.8 28.0 - - + -
1128A ARG* 4.1 24.5 - - + -
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Residues in contact with GLN1109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055A PHE* 3.6 24.9 - - + -
1107A PHE* 3.3 19.1 + - + -
1108A LEU* 1.3 75.3 - - - +
1110A PHE* 1.3 82.2 + - - +
1125A VAL* 4.1 15.0 - - + -
1126A THR 2.8 14.9 + - - +
1127A GLY* 3.5 1.4 - - - -
1128A ARG* 2.9 26.2 + - - +
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Residues in contact with PHE1110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1108A LEU* 3.8 33.4 + - + -
1109A GLN* 1.3 95.2 + - - +
1111A SER* 1.3 60.0 + - - +
1128A ARG* 3.5 38.6 - - + +
1129A PRO 5.3 0.4 - - - -
1130A SER* 4.5 18.2 - - - +
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Residues in contact with SER1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054A MET* 5.1 6.3 - - - -
1055A PHE* 3.9 29.5 - - - -
1109A GLN* 5.4 0.2 - - - -
1110A PHE* 1.3 76.5 - - - +
1112A ALA* 1.3 55.2 + - - +
1113A MET* 3.3 21.3 + - - +
1128A ARG 3.1 8.5 + - - -
1129A PRO* 3.4 18.0 - - - +
1130A SER* 2.7 36.3 + - - -
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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