Contacts of the strand formed by residues 1124 - 1129 (chain C) in PDB entry 4UVL
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 SER1124 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1103C LEU* 2.7 36.9 + - - +
1105C LYS 3.7 1.8 + - - +
1106C SER* 2.7 25.8 + - - -
1107C PHE* 2.9 23.7 + - - +
1118C SER* 3.5 6.3 + - - -
1122C HIS* 4.0 3.5 - - - +
1123C HIS* 1.3 79.0 - - - +
1125C VAL* 1.3 68.4 + - - +
1140C VAL 3.2 16.8 - - - -
1141C ILE* 4.1 7.9 - - - -
1142C TYR* 4.5 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055C PHE* 3.9 26.2 - - + +
1106C SER* 3.5 5.1 + - - -
1107C PHE* 3.4 15.7 - - + +
1109C GLN* 4.2 10.8 - - + +
1119C PRO* 3.7 27.4 - - + -
1124C SER* 1.3 80.6 - - - +
1126C THR* 1.3 70.9 + - - +
1127C GLY 4.0 0.3 + - - -
1139C TYR* 3.3 6.6 - - - +
1140C VAL* 2.9 34.2 + - + +
1142C TYR* 3.4 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1106C SER* 2.7 25.5 + - - -
1107C PHE 2.8 12.2 + - - -
1108C LEU* 4.0 21.7 - - + +
1109C GLN* 2.7 35.0 + - - +
1125C VAL* 1.3 71.5 - - - +
1127C GLY* 1.3 61.4 + - - +
1128C ARG* 4.6 4.3 - - + +
1137C ALA* 4.2 11.9 - - + -
1138C GLU 3.7 2.9 - - - -
1139C TYR* 3.3 34.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1055C PHE* 3.5 34.9 - - - -
1109C GLN 3.4 5.8 - - - -
1111C SER* 5.1 0.7 - - - -
1125C VAL* 3.9 2.6 - - - +
1126C THR* 1.3 71.4 - - - +
1128C ARG* 1.3 59.1 + - - -
1129C PRO* 3.5 6.0 - - - +
1137C ALA* 3.5 0.9 - - - -
1138C GLU* 2.7 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1108C LEU* 4.0 25.6 - - + -
1109C GLN 2.9 10.8 + - - +
1110C PHE* 3.4 28.5 - - + -
1111C SER* 2.9 23.2 + - - +
1126C THR* 3.7 4.9 + - + -
1127C GLY* 1.3 72.3 - - - +
1129C PRO* 1.3 80.5 + - + +
1130C SER 3.3 0.5 + - - -
1137C ALA* 4.6 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO1129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
977C ARG* 5.6 0.4 - - - +
1110C PHE* 5.2 0.7 - - - -
1111C SER* 3.7 12.3 - - - +
1113C MET* 3.5 24.0 - - + +
1127C GLY 3.5 7.9 - - - +
1128C ARG* 1.3 99.4 + - + +
1130C SER* 1.3 59.4 + - - +
1131C VAL 3.7 0.2 - - - -
1132C ASN 4.1 6.6 - - - +
1133C GLY* 5.8 0.9 - - - -
1135C ALA* 3.8 32.3 - - + +
1136C LEU 3.4 31.2 - - - +
1138C GLU* 4.5 11.9 - - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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