Contacts of the strand formed by residues 165 - 169 (chain L) in PDB entry 3GHG
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 GLY 165 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L HIS* 4.2 6.5 - - - -
163L GLN 3.8 2.4 + - - -
164L SER* 1.3 74.5 + - - +
166L LEU* 1.3 58.9 + - - -
167L TYR* 3.5 12.0 - - - -
181L TYR* 3.2 19.7 - - - -
182L CYS 2.8 39.4 + - - -
220L PRO* 4.0 10.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203K ILE* 4.6 17.0 - - + -
143L VAL* 4.8 4.7 - - + -
144L GLN 4.8 5.8 - - - +
145L ILE* 3.9 10.0 - - + +
146L HIS* 3.1 34.4 + - - -
165L GLY* 1.3 70.9 - - - -
167L TYR* 1.3 59.9 + - - +
179L LEU* 3.6 14.8 - - + -
180L VAL 3.4 10.5 - - - +
181L TYR* 4.0 8.5 - - + -
218L LEU* 2.9 49.8 - - + +
219L SER 3.6 7.9 - - - +
220L PRO* 3.5 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L HIS* 3.5 38.5 - + + -
148L ILE* 4.0 16.8 - - + -
156L ILE* 3.3 46.2 - - + -
161L ALA* 3.4 19.2 - - + +
163L GLN* 2.9 39.1 + - - +
165L GLY 3.5 17.7 + - - -
166L LEU* 1.3 79.7 - - - +
168L PHE* 1.3 61.8 + - - +
169L ILE* 4.6 0.7 - - + -
179L LEU* 2.9 7.8 - - - +
180L VAL* 2.9 33.9 + - - +
182L CYS* 4.0 19.5 - - + -
184L ILE* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 168 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226K LEU* 4.8 7.6 - - + -
234K LYS* 6.0 0.4 - - + -
235K PRO* 3.6 39.5 - - + -
145L ILE* 3.4 43.7 - - + -
146L HIS 4.2 5.1 + - - +
148L ILE 3.6 7.0 + - - +
149L THR* 2.8 35.6 + - - +
150L GLY 3.5 0.2 + - - -
156L ILE* 3.7 1.2 - - - +
167L TYR* 1.3 70.7 - - - +
169L ILE* 1.3 66.8 + - - +
177L GLN* 2.9 28.7 - - + +
178L PHE* 3.4 5.2 - - - +
179L LEU* 3.4 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149L THR* 4.3 0.9 - - - -
150L GLY 3.2 15.3 - - - +
151L LYS 4.5 1.1 - - - +
152L ASP* 4.0 21.1 - - - +
156L ILE* 3.5 22.7 - - + -
167L TYR 4.5 0.2 - - - +
168L PHE* 1.3 80.8 - - - +
170L LYS* 1.3 58.0 + - - +
171L PRO* 3.8 7.8 - - + +
177L GLN* 4.2 2.9 - - - -
178L PHE* 3.0 37.0 + - + -
180L VAL* 3.1 42.0 - - + -
192L THR* 4.1 8.5 - - + -
236L ILE* 3.8 25.6 - - + -
----------------------------------------------------------
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