Contacts of the strand formed by residues 177 - 184 (chain L) in PDB entry 1GC1
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 LEU 177 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H PHE* 3.6 6.4 - - - -
136L CYS 3.9 0.2 - - - +
137L LEU* 3.4 4.2 - - - +
138L LEU* 3.0 40.1 + - + +
141L PHE* 3.4 18.6 - - + -
144L ARG 5.2 2.7 - - - +
146L ALA* 4.6 14.1 - - + +
148L VAL* 3.9 23.1 - - + -
163L GLU* 3.5 37.5 - - + +
164L SER 3.1 13.0 - - - +
165L VAL* 3.7 17.9 - - + -
176L SER* 1.3 76.2 - - - +
178L SER* 1.3 81.9 + - - +
179L SER* 3.8 4.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 178 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181H PHE* 3.4 39.0 - - - +
194H SER* 4.9 11.8 + - - -
196H VAL* 6.4 0.2 - - - -
135L VAL* 4.9 7.9 - - - -
136L CYS 3.3 7.6 - - - -
137L LEU* 5.2 2.0 - - - -
162L GLN 3.7 2.8 - - - +
163L GLU* 3.0 3.6 - - - -
164L SER* 2.8 37.1 + - - -
177L LEU* 1.3 76.2 - - - +
179L SER* 1.3 60.0 + - - +
180L THR* 3.9 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135L VAL* 4.5 0.4 - - - -
136L CYS* 2.8 40.7 + - - -
138L LEU* 5.7 0.2 - - - -
148L VAL* 3.7 24.5 - - - +
150L TRP* 3.0 24.5 + - - -
161L SER* 4.2 9.4 - - - -
163L GLU* 3.3 27.2 + - - +
177L LEU* 3.8 7.9 - - - +
178L SER* 1.3 71.9 - - - +
180L THR* 1.3 58.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 180 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156H LEU* 4.5 10.8 - - + +
158H LYS* 6.2 2.0 - - - -
192H SER* 6.0 1.1 - - - +
194H SER* 4.8 6.4 + - - -
133L SER* 4.2 17.5 - - - -
134L VAL 3.2 17.3 - - - +
135L VAL* 3.9 20.4 - - + +
150L TRP* 4.5 0.4 - - - -
160L ASN 3.8 1.4 - - - +
161L SER* 3.2 6.7 - - - -
162L GLN* 3.2 37.3 + - - -
178L SER* 4.7 5.5 + - - -
179L SER* 1.3 73.3 + - - +
181L LEU* 1.3 62.8 + - - +
182L THR* 4.7 6.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132L ALA 3.9 0.9 - - - +
133L SER* 3.5 3.3 - - - -
134L VAL* 2.9 34.5 + - + +
150L TRP* 3.8 51.6 - - + -
151L LYS 4.6 5.4 - - - +
152L VAL* 5.9 0.4 - - - -
157L GLN* 4.2 16.6 - - + -
160L ASN* 3.0 32.8 - - - +
161L SER* 3.4 22.2 - - - +
179L SER 4.1 0.8 + - - -
180L THR* 1.3 74.1 - - - +
182L THR* 1.3 64.2 + - - +
183L LEU* 4.2 18.0 - - + +
194L TYR* 5.2 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 182 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H LYS* 4.9 11.0 - - - +
186H GLN* 5.4 3.6 + - - +
131L THR* 4.0 13.9 - - + -
132L ALA 3.6 3.6 - - - +
133L SER* 3.3 26.5 - - - +
160L ASN* 3.2 39.2 + - - +
180L THR* 4.7 7.7 + - + +
181L LEU* 1.3 75.4 + - - +
183L LEU* 1.3 67.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131L THR* 3.5 5.7 - - - +
132L ALA 2.8 33.3 + - - +
134L VAL* 4.1 15.9 - - + -
152L VAL* 4.2 10.8 - - + -
157L GLN* 6.4 0.7 - - + -
160L ASN* 5.7 3.1 - - - +
181L LEU* 4.2 15.9 - - + +
182L THR* 1.3 78.6 - - - +
184L SER* 1.3 69.5 + - - +
187L ASP* 3.4 36.1 - - - +
188L TYR* 3.6 26.0 - - + +
194L TYR* 3.9 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130L GLY 4.7 2.5 - - - -
131L THR* 4.5 8.1 - - - -
132L ALA 4.1 0.2 - - - -
183L LEU* 1.3 77.4 - - - +
185L LYS* 1.3 67.1 + - - +
186L ALA* 3.0 12.0 + - - +
187L ASP* 3.2 23.3 + - - +
188L TYR* 3.1 18.7 + - - +
----------------------------------------------------------
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