Contacts of the strand formed by residues 202 - 212 (chain A) in PDB entry 4IF8
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 MET 202 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 3.8 23.6 - - + -
139A PHE 3.3 3.6 - - - -
140A ILE* 3.7 30.3 - - + -
200A THR* 3.6 3.8 - - - +
201A VAL* 1.3 83.8 - - - +
203A LEU* 1.3 62.2 + - - +
338A LEU* 3.8 19.3 - - + -
341A ILE* 3.8 20.6 - - + -
347A LEU* 3.8 27.8 - - + -
348A LYS 3.6 23.2 + - - +
349A VAL* 3.7 16.2 - - + -
350A GLY* 2.8 30.2 + - - +
351A GLU 3.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A THR 3.7 0.5 - - - +
138A LEU* 3.4 4.7 - - - -
139A PHE* 2.7 54.9 + - + +
167A PHE* 3.9 15.7 - - + -
177A ILE* 4.0 17.5 - - + -
193A ILE* 3.8 27.4 - - + -
196A ILE* 4.1 20.2 - - + -
200A THR* 4.3 3.1 - - + -
202A MET* 1.3 73.7 - - - +
204A LEU* 1.3 73.1 + - - +
205A ALA* 4.1 2.7 - - + +
351A GLU* 3.3 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA* 3.8 24.5 - - + +
83A PHE* 4.2 13.2 - - + -
85A MET* 3.8 25.4 - - + -
86A LEU* 3.7 27.6 - - + -
136A ASN* 4.5 6.3 - - - +
137A THR 3.7 12.3 - - - +
138A LEU* 3.9 15.3 - - + -
203A LEU* 1.3 78.2 - - - +
205A ALA* 1.3 72.3 + - - +
206A ASN* 4.8 1.3 - - + +
319A LEU* 5.3 1.8 - - + -
349A VAL* 4.3 6.2 - - + +
351A GLU 2.8 10.6 + - - +
352A ALA* 3.2 14.3 - - + -
353A VAL 3.0 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ASN* 3.5 3.3 - - - -
137A THR 2.9 40.6 + - - +
139A PHE* 4.1 9.4 - - + -
181A ILE* 3.7 30.3 - - + -
192A LEU* 3.7 14.1 - - + -
203A LEU* 4.0 5.1 + - + -
204A LEU* 1.3 74.8 - - - +
206A ASN* 1.3 61.6 + - - +
207A TYR* 3.5 10.0 - - + -
353A VAL 3.7 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 2.7 47.5 + - - +
79A ILE* 3.8 1.8 + - - -
81A THR* 3.7 0.2 + - - -
82A ALA* 3.7 14.1 - - + +
134A ILE* 4.4 0.2 - - - +
135A GLY 3.3 8.7 + - - -
136A ASN* 2.8 29.2 + - - +
192A LEU* 4.7 1.4 - - - +
204A LEU* 4.1 2.2 - - + -
205A ALA* 1.3 73.6 - - - +
207A TYR* 1.3 62.1 + - - +
319A LEU* 4.6 7.0 - - + -
353A VAL 2.8 13.0 + - - +
354A HIS* 2.8 28.5 + - - +
355A LYS 3.0 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A SER* 4.1 2.5 + - - -
133A SER 3.9 0.7 - - - +
134A ILE* 3.6 0.9 - - - -
135A GLY* 2.7 54.5 + - - +
137A THR* 2.6 26.0 + - - -
180A PHE* 4.4 0.5 - - - -
181A ILE* 4.1 27.7 - - + +
184A LYS* 3.1 26.8 + - + +
185A THR* 3.7 31.9 - - + -
189A ILE* 3.8 21.1 - - + -
192A LEU* 4.9 2.5 - - + -
205A ALA* 3.5 31.2 - - + -
206A ASN* 1.3 81.8 - - - +
208A ILE* 1.3 63.5 + - - +
209A PHE* 5.8 1.3 - + - -
355A LYS* 3.2 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A SER* 3.4 38.6 - - - +
77A LEU* 5.3 2.0 - - + -
78A SER* 3.8 13.5 - - - +
132A LEU* 4.2 11.9 - - + -
133A SER 3.4 14.8 - - - +
134A ILE* 3.8 23.6 - - + -
189A ILE* 3.6 6.2 - - - +
207A TYR* 1.3 75.5 - - - +
209A PHE* 1.3 67.7 + - - +
354A HIS* 4.1 1.1 - - + -
355A LYS 3.0 4.3 + - - +
356A ALA* 3.5 10.1 - - + -
357A GLU 2.9 25.5 + - - +
403A LEU* 4.2 8.3 - - + +
404A PHE* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN 5.6 0.4 - - - -
131A LYS* 4.0 22.9 - - + -
132A LEU* 3.5 15.9 - - - +
133A SER* 3.4 45.4 + - - -
184A LYS 5.4 0.9 - - - -
185A THR* 3.9 43.7 - - + -
186A HIS* 6.0 2.0 - - - -
188A LYS* 3.4 36.1 - - + -
189A ILE* 4.3 7.6 - - + -
207A TYR* 5.8 1.3 - + - -
208A ILE* 1.3 79.8 - - - +
210A PHE* 1.3 63.9 + - - +
357A GLU* 3.2 22.2 - - - +
404A PHE* 4.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 3.7 25.6 - - + -
131A LYS 3.4 4.7 - - - -
132A LEU* 4.1 11.2 - - + -
209A PHE* 1.3 77.4 - - - +
211A ARG* 1.3 85.2 + - - +
212A ALA* 3.4 24.9 - - + -
264A TYR* 3.6 41.7 - + - -
268A ILE* 4.1 12.8 - - + -
357A GLU* 3.1 7.1 + - - +
358A LEU* 3.6 21.3 - - + -
359A LYS 3.5 16.1 + - - +
394A ILE* 4.0 12.6 - - + -
403A LEU* 4.3 3.8 - - + -
404A PHE* 3.4 29.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A LEU* 3.4 3.2 - - - +
131A LYS* 2.8 52.9 + - + +
188A LYS* 3.7 32.6 - - - +
209A PHE* 5.5 0.2 - - + -
210A PHE* 1.3 100.1 + - - +
212A ALA* 1.3 64.2 + - - +
312A HIS* 4.1 1.0 + - - -
357A GLU* 2.6 45.2 + - - -
359A LYS* 3.7 39.8 - - - +
363A ARG* 3.8 15.9 - - - +
501A SO4 3.2 41.1 + - - +
183B GLN* 5.7 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ASP 3.2 12.3 - - - +
130A LEU* 3.9 7.9 - - + -
210A PHE* 3.4 30.5 - - + -
211A ARG* 1.3 76.3 - - - +
213A ARG* 1.3 66.0 + - - +
214A TRP* 3.8 1.9 + - - -
264A TYR* 3.5 26.1 - - + -
266A LYS* 6.3 0.7 - - + -
268A ILE* 5.5 0.4 - - + -
359A LYS 5.4 2.5 + - - +
363A ARG* 3.4 21.8 - - - +
----------------------------------------------------------
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