Contacts of the strand formed by residues 160 - 165 (chain I) in PDB entry 3CII
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 ASN 160 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A GLN* 5.4 4.9 - - - +
76D VAL* 3.9 23.8 - - + +
8F PHE* 3.2 38.5 - - - -
114I PHE* 3.5 9.3 - - + -
142I PRO* 5.3 5.6 - - - -
155I TYR* 3.5 5.8 - - - -
156I ASN* 2.9 35.3 + - - +
158I ASN* 3.5 25.6 + - - +
159I GLY* 1.3 78.2 - - - +
161I ALA* 1.3 59.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 5.0 1.6 - - - +
114I PHE* 4.1 0.4 - - - -
141I PHE* 4.4 22.2 - - + -
142I PRO* 5.5 4.0 - - + +
147I PHE* 4.0 22.3 - - + -
153I ILE* 3.7 18.6 - - + -
154I ALA 3.1 10.5 - - - +
155I TYR* 4.7 1.3 - - + -
159I GLY 4.0 1.0 + - - -
160I ASN* 1.3 78.4 - - - +
162I LEU* 1.3 74.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLN* 3.5 37.9 - - + +
75D ARG* 3.4 46.7 - - + +
76D VAL* 3.9 16.2 - - + -
79D ARG* 5.1 10.1 - - - +
114I PHE* 3.9 22.7 - - + -
147I PHE* 4.9 0.4 - - - -
153I ILE* 3.4 3.7 - - - -
154I ALA* 2.7 45.2 + - + +
161I ALA* 1.3 83.6 - - - +
163I ASP* 1.3 60.9 + - - +
164I GLU* 3.5 11.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 163 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG* 3.1 32.6 + - - +
79D ARG* 3.8 11.4 + - - -
146I THR 4.6 1.0 - - - +
147I PHE* 3.6 32.0 - - + -
148I ASN* 2.8 33.1 + - - +
151I ASN* 4.0 16.4 + - + -
152I CYS 3.3 6.7 - - - +
153I ILE* 3.8 11.2 - - + -
162I LEU* 1.3 70.7 - - - +
164I GLU* 1.3 61.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D GLU* 4.1 16.6 - - - +
72D GLN* 2.8 34.0 + - - +
75D ARG* 4.0 15.7 - - - +
114I PHE* 5.5 0.2 - - - +
116I TRP* 4.1 14.6 - - + -
151I ASN* 3.0 11.5 - - - +
152I CYS* 2.8 34.2 + - - +
154I ALA* 4.7 7.1 - - - +
162I LEU* 3.5 12.8 + - + +
163I ASP* 1.3 75.4 - - - +
165I SER* 1.3 62.2 + - - +
168I ASP* 3.9 16.5 - - + +
170I ASN* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 165 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I TRP* 3.8 10.5 - - - -
151I ASN* 3.2 11.6 + - - +
164I GLU* 1.3 76.8 - - - +
166I CYS* 1.3 55.5 + - - +
167I GLU* 2.7 26.8 + - - +
168I ASP* 3.0 31.7 + - - +
----------------------------------------------------------
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