Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 3KSS
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 VAL 174 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 4.1 8.1 - - + +
169A LYS* 4.0 10.3 - - - +
171A ILE* 3.4 40.7 - - + +
172A PRO 3.2 4.8 - - - +
173A ASP* 1.3 76.4 - - - +
175A ALA* 1.3 66.2 + - - +
176A GLU 4.0 6.3 - - - +
177A VAL* 3.7 30.1 - - + -
289A VAL* 3.9 16.4 - - + -
290A ILE 3.5 11.2 - - - +
292A ARG* 4.9 0.7 - - - -
300A VAL* 3.5 22.0 - - + -
304A VAL* 4.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 4.8 4.0 - - + -
132A ASP* 4.4 16.4 - - + +
133A ALA* 4.7 2.5 - - + +
169A LYS* 4.0 13.2 - - - +
173A ASP 3.3 4.6 + - - -
174A VAL* 1.3 75.3 - - - +
176A GLU* 1.3 62.5 + - + +
290A ILE* 2.8 24.2 + - + +
291A LEU 4.5 0.4 - - - -
292A ARG* 3.9 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PRO* 3.7 27.6 - - + +
165A LYS* 5.4 6.3 + - - -
169A LYS* 4.8 12.1 - - - +
174A VAL* 4.0 1.9 - - - +
175A ALA* 1.3 82.0 - - + +
177A VAL* 1.3 64.1 + - - +
178A ALA* 4.6 1.6 - - - +
290A ILE* 3.2 39.3 + - + +
613A GLU 4.9 2.2 - - - +
614A THR* 3.1 44.3 - - - +
615A ALA* 4.0 3.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 4.5 6.3 - - + +
160A GLN* 3.8 17.3 - - - +
165A LYS* 2.9 46.6 - - + +
168A LEU* 3.6 32.5 - - + -
169A LYS* 3.9 12.3 - - + +
174A VAL* 3.7 22.4 - - + -
176A GLU* 1.3 72.2 - - - +
178A ALA* 1.3 69.2 + - - +
288A VAL 3.2 12.1 - - - +
289A VAL* 4.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TRP* 5.3 0.7 - - + -
160A GLN* 3.9 0.2 + - - -
165A LYS* 4.2 1.3 - - - +
176A GLU* 3.7 4.8 + - - +
177A VAL* 1.3 79.6 - - - +
179A SER* 1.3 60.6 + - - +
287A GLY* 3.0 6.6 - - - -
288A VAL* 2.7 56.9 + - + +
290A ILE* 4.7 1.3 - - + -
612A ALA 3.8 5.4 - - - +
613A GLU 3.7 3.4 - - - -
614A THR* 2.8 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A ARG* 3.0 32.1 + - - -
160A GLN* 2.6 26.0 + - - -
161A ASP* 2.9 10.7 + - - -
165A LYS* 3.4 17.6 + - - +
177A VAL 3.5 0.2 + - - -
178A ALA* 1.3 72.7 - - - +
180A VAL* 1.3 60.6 + - - +
286A GLY 3.7 0.9 - - - -
612A ALA* 3.1 2.6 - - - -
613A GLU* 3.1 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLU* 6.1 0.2 - - - +
142A TYR 5.3 0.2 - - - +
157A ARG* 5.0 1.7 + - - +
179A SER* 1.3 74.3 - - - +
181A GLY* 1.3 69.3 + - - +
274A GLY 5.9 0.2 - - - -
275A ILE 5.3 0.7 - - - -
276A ALA* 3.5 21.5 - - + +
285A ALA* 3.6 1.7 - - - +
286A GLY* 2.9 53.3 + - - +
287A GLY* 3.4 11.9 - - - +
288A VAL* 4.6 7.9 - - + +
606A PHE* 4.8 11.2 - - + -
608A LYS* 3.8 24.9 - - + -
611A LYS 4.9 1.8 - - - +
612A ALA* 3.7 17.7 - - + +
----------------------------------------------------------
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