Contacts of the strand formed by residues 170 - 178 (chain A) in PDB entry 6KSF
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 TRP 170 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 3.7 18.4 - - + -
129A SER* 3.3 34.6 - - - -
130A ASN* 3.2 31.9 + - + +
133A LYS* 5.1 7.9 - - + -
168A LEU* 4.1 0.7 - - - +
169A ARG* 1.3 88.7 - - + +
171A VAL* 1.3 80.9 + - - +
172A THR* 3.9 17.0 - - + -
218A ILE* 5.0 0.9 - - + -
219A LEU 3.0 12.6 - - - +
220A ASN* 3.9 12.3 - - - +
221A TYR* 3.9 2.1 - - - -
10B C 3.5 51.2 + - + +
11B C 3.8 9.6 - - - -
12B G 3.6 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR 3.4 25.4 - - - +
123A SER* 4.3 5.4 - - - -
127A ASN* 3.9 4.9 - - + -
128A VAL 3.5 9.2 - - - +
129A SER* 3.8 14.8 - - - -
168A LEU* 4.0 6.1 - - + -
170A TRP* 1.3 83.0 - - - +
172A THR* 1.3 76.3 + - - +
173A LEU* 3.9 11.0 - - + -
217A GLY 3.8 0.3 - - - +
218A ILE* 3.4 6.7 - - - +
219A LEU* 2.9 44.1 + - + +
221A TYR* 3.8 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ASN* 4.0 7.4 - - - +
128A VAL* 3.0 28.0 + - - +
170A TRP* 3.9 16.4 - - + -
171A VAL* 1.3 79.5 - - - +
173A LEU* 1.3 71.3 + - - +
175A TYR 5.7 0.2 - - - -
176A HIS* 3.1 34.2 + - + -
190A THR* 4.3 3.3 + - - -
217A GLY 3.5 6.5 - - - +
218A ILE* 5.4 0.4 - - + -
10B C 3.7 33.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A TYR* 4.5 4.7 - - + +
127A ASN* 3.4 33.2 - - - +
171A VAL* 3.9 11.0 - - + -
172A THR* 1.3 83.9 - - - +
174A GLY* 1.3 66.3 + - - +
175A TYR 3.6 4.6 + - - +
176A HIS* 4.9 0.4 - - - -
190A THR* 4.3 3.1 - - - -
191A PRO 5.5 0.2 - - - -
192A PHE* 3.9 16.6 - - + -
193A PRO* 4.0 26.7 - - + -
196A LEU* 4.1 21.3 - - + -
216A ALA* 3.5 2.1 - - - -
217A GLY* 2.9 38.1 + - - +
219A LEU* 4.1 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU* 1.3 71.0 - - - +
175A TYR* 1.3 65.8 + - - -
176A HIS* 3.6 9.2 + - - -
189A TYR* 3.5 14.9 - - - -
190A THR* 3.0 40.1 + - - -
191A PRO 4.5 0.2 - - - -
192A PHE* 4.0 12.3 - - - +
215A GLU 3.3 11.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A THR* 5.7 0.5 - - - -
173A LEU 3.7 8.0 - - - +
174A GLY* 1.3 74.0 - - - -
176A HIS* 1.3 62.4 + - - +
184A TYR* 3.8 19.3 - - + -
185A SER 3.4 20.6 - - - +
186A ALA* 4.2 9.0 - - + -
189A TYR* 3.7 33.4 - + - -
215A GLU* 3.1 31.9 + - + +
216A ALA* 3.7 12.2 - - + +
217A GLY 5.0 0.2 + - - -
346A VAL* 3.8 19.5 - - + -
347A LEU* 3.3 28.1 - - + +
352A ASP* 4.4 9.7 + - - -
353A PHE* 3.4 25.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 4.1 22.6 - - + +
172A THR* 3.1 41.8 + - + -
174A GLY 3.6 14.8 + - - -
175A TYR* 1.3 77.3 - - - +
177A TYR* 1.3 65.5 + - - +
178A ASN* 3.9 0.5 + - - +
184A TYR* 3.6 3.9 - - - -
185A SER* 3.5 30.3 + - - +
187A ASP 4.6 9.6 + - - +
188A HIS* 2.9 35.3 + - + +
189A TYR* 5.6 0.4 - - - +
190A THR* 3.8 15.4 + - + -
10B C 5.7 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS* 1.3 77.4 - - - +
178A ASN* 1.3 68.1 + - - +
179A TRP* 3.6 50.6 + + + +
182A LYS* 3.2 55.5 - - - +
183A LYS* 3.5 7.0 - - - -
184A TYR* 3.6 32.8 - + + -
234A ARG* 5.6 0.2 - - - +
235A CYS* 3.5 22.9 + - + +
10B C 4.1 18.8 + - + +
101B XL3 3.5 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS 3.9 1.1 + - - +
177A TYR* 1.3 75.1 - - - +
179A TRP* 1.3 59.2 + - - +
180A ASP* 2.8 39.0 + - - +
181A SER* 2.8 27.6 + - - +
182A LYS* 2.9 30.5 + - - -
183A LYS 3.0 21.1 + - - +
185A SER* 5.6 8.9 + - - +
----------------------------------------------------------
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