Contacts of the strand formed by residues 172 - 181 (chain I) in PDB entry 1K9O
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 SER 172 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106I ILE* 4.8 7.4 - - - -
107I TYR 3.1 12.1 - - - -
108I VAL* 4.2 13.2 - - - -
135I PHE* 3.9 0.9 - - - -
170I THR 3.6 1.0 - - - -
171I ARG* 1.3 81.8 - - - +
173I VAL* 1.3 63.4 + - - +
312I LEU* 5.0 2.4 - - - +
315I LEU* 5.9 0.4 - - - -
322I LEU* 4.5 6.8 - - - +
323I THR 2.5 28.4 + - - -
324I VAL* 3.1 14.3 - - - +
325I ASP* 2.7 38.8 + - - +
326I ALA 3.4 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 173 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I LYS 3.7 1.2 - - - +
106I ILE* 3.6 6.2 - - - +
107I TYR* 3.1 34.3 + - + +
135I PHE* 3.6 17.9 - - + -
145I ILE* 5.0 5.6 - - + -
161I VAL* 5.4 4.0 - - + -
166I LEU* 4.4 9.4 - - + -
170I THR* 3.5 23.6 - - + -
172I SER* 1.3 79.2 - - - +
174I LEU* 1.3 65.3 + - - +
175I VAL* 3.9 24.0 + - + -
324I VAL* 4.9 1.1 - - - -
326I ALA* 3.4 29.6 - - + +
327I ALA 4.7 0.2 - - - +
328I ILE* 5.2 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I VAL* 5.2 3.4 - - + -
53I PRO* 3.7 35.2 - - + -
54I LEU* 4.9 10.1 - - + -
56I GLN* 5.9 0.4 - - - +
57I LEU* 4.3 17.0 - - + -
105I LYS 3.6 16.6 - - - +
106I ILE* 4.2 16.8 - - + +
173I VAL* 1.3 73.1 - - - +
175I VAL* 1.3 66.0 + - - +
176I ASN* 5.4 2.0 - - + -
292I LEU* 4.7 13.2 - - + -
296I LEU* 5.4 2.5 - - + -
304I LEU* 5.7 2.7 - - + -
305I PHE* 5.8 0.7 - - + -
324I VAL* 4.8 7.0 - - + -
326I ALA 2.9 14.6 + - - +
327I ALA* 3.1 13.8 - - + -
328I ILE 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I SER* 3.4 4.9 - - - -
105I LYS* 3.1 32.4 + - + +
107I TYR* 3.5 29.2 - - + -
145I ILE* 3.4 23.8 - - + -
148I TRP* 4.6 2.6 - - + -
149I VAL* 4.3 14.4 - - + -
160I LEU* 3.3 27.8 - - + -
161I VAL* 5.1 3.6 - - + -
173I VAL* 3.9 19.0 - - + -
174I LEU* 1.3 76.5 - - - +
176I ASN* 1.3 60.8 + - - +
328I ILE* 4.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 176 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I SER* 3.5 18.6 + - - +
50I VAL* 3.1 19.7 - - - +
53I PRO* 5.7 1.3 - - + -
103I ALA 2.8 24.2 - - - +
104I SER* 3.1 11.8 + - - +
149I VAL* 6.0 0.2 - - - -
160I LEU* 3.3 7.9 - - - +
174I LEU* 5.1 4.3 - - + +
175I VAL* 1.3 75.7 - - - +
177I ALA* 1.3 65.0 + - - +
178I ILE* 4.8 0.2 - - - +
292I LEU* 4.2 6.7 - - + -
328I ILE 3.1 15.5 + - - +
329I GLN* 2.9 40.4 - - - +
330I LYS 3.0 24.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 177 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I LYS 3.2 3.8 - - - +
102I MET* 3.5 1.0 - - - -
103I ALA* 2.7 48.4 + - + +
149I VAL* 3.6 32.3 - - + +
153I THR* 4.1 8.7 - - + -
157I ILE* 3.7 13.9 - - + -
160I LEU* 4.1 2.9 - - + -
176I ASN* 1.3 76.0 + - - +
178I ILE* 1.3 63.6 + - - +
330I LYS 3.5 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 178 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I SER* 3.5 37.0 - - - +
49I SER* 4.0 8.5 - - - +
100I LEU* 3.3 33.2 - - + -
101I LYS 3.1 4.9 - - - +
102I MET* 3.7 9.0 - - + -
157I ILE* 3.4 5.4 - - - +
176I ASN* 4.8 0.7 - - - +
177I ALA* 1.3 78.4 - - - +
179I TYR* 1.3 62.1 + - - +
180I PHE* 5.6 0.7 - - + -
329I GLN* 4.2 11.4 - - + +
330I LYS 3.1 11.9 + - - +
331I ALA* 3.3 19.4 - - + -
332I PHE 3.0 24.1 + - - -
379I PHE* 3.6 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I ASP* 3.3 30.5 + - - +
100I LEU* 3.3 6.2 - - - +
101I LYS* 2.9 58.9 + - + -
153I THR* 4.6 2.0 - - + -
156I ARG* 3.4 55.8 + - + -
157I ILE* 4.5 7.0 - - + -
178I ILE* 1.3 77.1 - - - +
180I PHE* 1.3 65.8 + - - +
181I LYS* 3.1 38.6 - - + +
332I PHE* 3.4 39.0 - + + -
334I GLU* 3.7 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98I VAL* 3.3 40.4 - - + -
99I ASP 3.6 4.9 - - - -
100I LEU* 4.3 8.3 - - + -
178I ILE* 5.5 1.1 - - + -
179I TYR* 1.3 80.0 - - - +
181I LYS* 1.3 65.6 + - - +
182I GLY 3.8 13.7 - - - -
234I TYR* 3.4 23.6 - + - -
241I MET* 5.3 2.2 - - + -
332I PHE 3.0 13.5 + - - +
333I ILE* 3.5 21.0 - - + -
334I GLU* 2.9 30.2 + - - +
335I VAL* 5.4 0.9 - - + -
371I LEU* 3.3 31.4 - - + -
379I PHE* 3.1 37.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 181 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99I ASP* 3.1 32.5 + - + +
156I ARG* 5.6 7.0 - - - +
179I TYR* 3.1 31.9 - - + +
180I PHE* 1.3 78.5 - - - +
182I GLY* 1.3 59.4 + - - +
334I GLU* 3.6 36.6 + - + +
336I ASN* 3.4 23.5 - - - +
338I GLU* 2.9 37.2 + - - +
----------------------------------------------------------
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