Contacts of the strand formed by residues 114 - 119 (chain A) in PDB entry 3PE7
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 GLU 114 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 2.7 38.0 + - - +
76A THR* 3.8 11.6 - - - +
77A GLU 5.0 1.0 + - - -
97A TYR* 2.6 33.9 + - - -
99A LYS* 3.7 7.7 + - - +
105A MET* 3.6 20.9 - - + +
106A ARG 3.2 6.7 - - - +
107A VAL* 3.6 14.4 - - + -
112A LEU 3.7 0.4 - - - +
113A GLU* 1.3 77.3 - - - +
115A ASN* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A MET* 3.4 5.8 - - - -
106A ARG* 2.9 40.9 + - + +
114A GLU* 1.3 76.4 - - - +
116A VAL* 1.3 83.4 + - - +
117A VAL* 3.4 12.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ASN* 4.4 17.3 - - + +
104A LEU 3.7 4.3 - - - +
105A MET* 3.7 22.2 - - + +
115A ASN* 1.3 83.6 + - - +
117A VAL* 1.3 61.5 + - - +
118A TYR* 3.9 23.8 - - - +
119A GLN* 4.5 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 4.4 9.9 - - + -
104A LEU* 2.7 23.7 + - + +
106A ARG* 3.8 32.5 - - + +
115A ASN* 4.1 13.9 - - - +
116A VAL* 1.3 76.5 - - - +
118A TYR* 1.3 61.4 + - + +
173A VAL* 4.8 2.0 - - + -
174A ASP 4.5 4.3 - - - +
175A LEU* 3.7 48.0 - - + +
178A GLY* 3.7 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG 3.7 1.1 - - - +
103A ASN* 3.7 1.7 - - - -
104A LEU* 2.8 41.7 + - + +
116A VAL* 3.5 6.0 - - - +
117A VAL* 1.3 81.6 - - + +
119A GLN* 1.3 73.4 + - - +
120A VAL* 3.8 14.6 - - + -
121A PRO* 3.3 14.8 - - + +
130A TRP* 3.9 17.7 - + - -
139A LEU* 6.6 0.2 - - + -
143A GLU* 2.5 32.8 + - - -
169A ARG* 4.5 0.7 + - - -
171A MET* 4.3 4.4 - - + +
173A VAL* 3.8 31.6 - - + -
178A GLY 3.9 17.5 - - - -
180A SER* 3.6 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG* 3.4 19.4 - - + +
103A ASN* 2.7 30.7 + - - +
116A VAL* 4.5 8.2 - - + +
118A TYR* 1.3 86.8 - - - +
120A VAL* 1.3 80.5 + - - +
121A PRO* 3.2 10.8 - - + +
----------------------------------------------------------
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