Contacts of the strand formed by residues 1076 - 1080 (chain E) in PDB entry 3F5P
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 LEU1076 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
996E ARG* 4.2 23.8 - - + +
999E ILE* 4.0 29.4 - - + -
1001E MET* 4.3 10.3 - - - -
1032E ILE* 3.7 17.7 - - + -
1033E LYS 3.5 0.7 - - - +
1034E THR* 3.5 32.3 - - + -
1068E VAL* 3.1 10.2 - - - +
1069E VAL* 2.8 59.7 + - + -
1074E PRO* 3.2 12.2 + - + +
1075E THR* 1.3 73.2 - - - +
1077E VAL* 1.3 61.6 + - - +
1078E ILE* 4.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1077 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E 741 3.4 29.0 - - - +
1032E ILE* 3.3 6.9 - - - +
1033E LYS* 2.9 37.2 + - + +
1035E VAL* 4.8 2.9 - - + -
1047E PHE* 3.0 42.2 - - + -
1048E LEU* 6.2 0.7 - - + -
1051E ALA* 5.1 4.5 - - + -
1065E LEU* 4.2 25.4 - - + -
1067E GLY 4.0 2.5 - - - +
1068E VAL* 4.3 8.5 - - + -
1075E THR* 5.0 2.7 - - + +
1076E LEU* 1.3 76.3 - - - +
1078E ILE* 1.3 63.4 + - - +
1079E MET* 4.0 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1078 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
994E VAL* 4.2 11.7 - - + -
999E ILE* 3.4 33.0 - - + -
1018E ALA* 4.3 7.0 - - + -
1021E VAL* 5.1 2.7 - - + -
1030E VAL* 3.8 32.5 - - + -
1031E ALA 3.5 2.5 - - - -
1032E ILE* 3.9 22.4 - - + -
1065E LEU* 3.8 2.9 - - - +
1066E LEU* 2.8 44.1 + - + -
1067E GLY 2.7 25.6 + - - +
1069E VAL* 3.8 19.7 - - + +
1076E LEU* 4.8 1.3 - - + -
1077E VAL* 1.3 76.8 - - - +
1079E MET* 1.3 56.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1079 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E 741 3.2 87.0 - - + +
1030E VAL* 3.4 6.6 - - - +
1031E ALA 2.8 31.4 + - - +
1054E MET* 4.6 9.0 - - + -
1063E VAL* 3.9 23.6 - - + +
1064E ARG 3.8 11.9 - - - +
1065E LEU* 3.3 34.8 - - - +
1066E LEU* 4.2 3.8 - - - -
1077E VAL* 4.5 2.2 - - + -
1078E ILE* 1.3 76.0 - - - +
1080E GLU* 1.3 59.1 + - - +
1081E LEU 3.4 0.3 + - - -
1152E GLY 5.3 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1080 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E 741 3.3 16.3 - - - -
1029E ARG 4.8 0.7 - - - -
1062E VAL 4.0 1.0 - - - +
1063E VAL* 3.8 10.2 - - + +
1064E ARG* 3.0 49.4 + - + +
1066E LEU* 3.9 17.0 - - + +
1079E MET* 1.3 72.5 - - - +
1081E LEU* 1.3 73.7 + - - +
1082E MET* 3.5 11.3 + - - +
1150E LYS* 2.7 37.8 + - - +
----------------------------------------------------------
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