Contacts of the strand formed by residues 183 - 191 (chain H) in PDB entry 6IAP
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 TYR 183 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H THR* 5.3 6.2 - - + +
151H ASP* 2.9 27.4 + - - -
152H TYR* 3.0 43.7 + - + +
153H PHE* 3.6 29.8 - + - -
154H PRO* 4.2 1.8 - - + -
155H GLU* 4.0 35.3 - - + +
175H ALA* 4.0 17.9 - - + -
176H VAL 3.9 2.9 - - - -
177H LEU* 3.6 42.9 - - + +
178H GLN* 3.8 0.6 - - - +
182H LEU* 1.3 71.6 - - - +
184H SER* 1.3 59.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 184 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H LEU* 3.5 22.5 - - - +
149H VAL 3.3 9.6 - - - -
150H LYS* 3.9 9.3 - - - +
152H TYR* 4.0 1.1 - - - -
175H ALA* 3.3 4.9 - - - +
176H VAL* 3.0 32.5 + - - -
178H GLN* 3.7 25.7 + - - -
183H TYR* 1.3 74.4 - - - +
185H LEU* 1.3 72.0 + - - +
186H SER* 5.3 0.2 + - - -
160L GLN* 5.5 1.1 - - - -
178L THR* 5.5 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 185 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148H LEU* 3.3 6.6 - - - +
149H VAL* 2.8 39.0 + - + +
152H TYR* 3.6 19.7 - - - +
155H GLU* 4.5 2.5 - - - +
157H VAL* 3.8 17.9 - - + -
159H VAL* 3.8 29.4 - - + -
172H THR* 3.8 14.8 - - + -
173H PHE* 3.2 26.0 - - - +
174H PRO 5.1 2.7 - - - -
175H ALA* 3.7 16.2 - - + +
184H SER* 1.3 76.5 + - - +
186H SER* 1.3 75.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 186 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H LEU* 4.2 14.8 - - - -
147H CYS 3.3 10.8 - - - -
148H LEU* 3.9 14.0 - - - +
149H VAL 4.5 0.2 - - - +
173H PHE* 3.1 45.7 + - - +
185H LEU* 1.3 85.3 + - - +
187H SER* 1.3 59.3 + - - +
188H VAL* 3.9 1.1 - - - -
133L VAL* 4.4 8.7 - - - +
176L SER* 4.9 8.1 + - - -
178L THR* 4.2 12.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H LEU* 4.6 0.5 - - - +
146H GLY* 3.1 4.3 - - - -
147H CYS 3.0 31.9 + - - -
159H VAL* 3.6 30.9 - - - +
161H TRP* 2.8 27.4 + - - -
170H VAL* 3.6 3.8 - - - +
171H HIS 3.4 3.6 - - - -
172H THR* 2.9 26.4 + - - +
185H LEU* 4.8 1.0 - - - +
186H SER* 1.3 72.4 - - - +
188H VAL* 1.3 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H LEU* 5.1 6.3 - - + -
144H ALA* 5.0 0.2 - - + -
145H LEU 3.1 23.1 - - - +
146H GLY* 4.6 0.9 - - - -
169H GLY 3.8 1.1 - - - +
170H VAL* 3.3 3.9 - - - +
171H HIS* 2.7 51.9 + - + -
173H PHE* 3.8 16.8 - - + -
186H SER* 3.9 1.5 - - - -
187H SER* 1.3 75.1 - - - +
189H VAL* 1.3 60.8 + - - +
190H THR* 5.7 0.7 - - + +
118L PHE* 4.3 11.7 - - + -
133L VAL* 6.5 0.4 - - + -
135L LEU* 3.3 48.7 - - + -
137L ASN* 4.7 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145H LEU* 2.7 55.7 + - + +
161H TRP* 3.8 34.1 - - + -
166H LEU* 4.0 21.1 - - + -
168H SER 4.0 8.7 - - - +
169H GLY 3.7 3.1 - - - -
170H VAL* 3.6 30.1 - - + +
188H VAL* 1.3 74.8 - - - +
190H THR* 1.3 77.1 + - - +
191H VAL* 4.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H THR* 4.4 10.8 - - - +
143H ALA 3.2 11.7 - - - +
144H ALA* 4.3 14.8 - - + -
166H LEU* 5.5 0.3 - - - +
168H SER 4.4 6.6 - - - +
169H GLY* 3.5 20.4 + - - +
171H HIS* 5.8 0.6 + - + -
188H VAL* 5.9 0.7 - - + -
189H VAL* 1.3 89.2 - - - +
191H VAL* 1.3 59.9 + - - +
116L PHE* 4.4 7.4 - - + -
135L LEU* 5.2 2.5 - - + -
137L ASN* 3.6 34.8 + - - +
138L ASN* 5.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H THR* 3.7 5.2 + - - -
143H ALA* 2.7 36.6 + - + +
145H LEU* 3.6 22.7 - - + -
166H LEU* 4.4 6.1 - - + -
189H VAL* 4.4 10.3 - - + -
190H THR* 1.3 77.2 - - - +
192H PRO* 1.4 78.8 - - + +
195H SER* 3.5 5.6 - - - +
196H LEU* 4.3 7.4 - - + -
201H TYR* 3.2 52.5 - - + +
----------------------------------------------------------
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