Contacts of the strand formed by residues 132 - 142 (chain B) in PDB entry 3AFF
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 GLY 132 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B VAL* 3.6 3.8 - - - +
129B VAL* 2.9 27.0 + - - +
130B ASP 3.3 2.2 + - - -
131B GLY* 1.3 80.3 - - - +
133B TYR* 1.3 76.7 + - - -
201B PHE* 3.8 2.7 - - - -
202B VAL 3.1 12.8 - - - -
204B ARG* 3.7 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B GLY* 4.0 9.6 - - - -
127B VAL 3.1 9.0 - - - +
128B VAL* 4.1 14.4 - - + -
129B VAL* 3.7 7.4 - - - +
132B GLY* 1.3 78.7 - - - -
134B LEU* 1.3 59.8 + - - +
135B VAL* 3.9 3.5 + - + -
157B VAL* 3.6 34.9 - - + +
165B ASP* 5.5 0.5 + - - -
169B PHE* 3.7 30.5 - + + -
200B VAL 3.5 1.0 - - - +
201B PHE* 3.4 4.0 - - - -
202B VAL* 2.8 43.0 + - + +
204B ARG* 3.8 36.8 - - + +
207B PHE* 3.5 41.3 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A GLY 5.2 0.3 - - - +
125B ALA 3.7 1.9 - - - +
126B GLY* 3.4 1.0 - - - -
127B VAL* 2.8 41.1 + - + +
129B VAL* 3.7 24.1 - - + +
133B TYR* 1.3 72.3 - - - +
135B VAL* 1.3 60.2 + - - +
136B ASN* 4.1 8.6 + - - +
199B ASP* 3.7 51.1 - - + +
200B VAL 3.6 6.3 - - - -
201B PHE* 4.1 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ALA 3.4 8.5 - - - +
126B GLY* 3.9 8.7 - - - -
133B TYR* 4.2 4.0 - - + -
134B LEU* 1.3 75.3 - - - +
136B ASN* 1.3 64.2 + - - +
139B TRP* 3.7 25.6 - - + -
153B VAL* 4.3 5.2 - - + -
169B PHE* 3.7 31.4 - - + -
171B ILE* 4.1 11.9 - - + -
197B VAL* 3.6 19.4 - - + +
199B ASP 3.3 6.9 + - - -
200B VAL 2.9 32.5 + - - +
202B VAL* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP 3.5 26.6 + - - +
161A GLY* 3.9 16.2 - - - +
162A ARG* 4.0 4.3 - - + +
124B GLY* 3.1 2.6 - - - -
125B ALA 3.1 28.2 + - - -
134B LEU* 4.4 12.1 + - - +
135B VAL* 1.3 78.5 + - - +
137B GLY* 1.3 58.7 + - - +
139B TRP* 3.6 6.0 - - - -
197B VAL 3.3 5.1 - - - +
198B LYS* 3.5 9.5 - - - +
199B ASP* 2.9 43.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 4.3 11.2 - - - -
123B MET 3.5 9.0 - - - -
124B GLY* 3.9 1.6 - - - -
136B ASN* 1.3 75.6 - - - +
138B SER* 1.3 60.7 + - - -
139B TRP* 3.4 16.6 - - - -
196B VAL* 3.8 3.1 - - - +
197B VAL 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ARG* 3.6 14.0 + - - +
123B MET* 3.2 26.2 + - - +
137B GLY* 1.3 74.2 - - - -
139B TRP* 1.3 59.7 + - - +
140B ASN* 4.0 0.5 + - - +
179B LYS* 5.1 3.6 + - - -
194B THR* 3.3 23.2 - - - +
195B LEU 3.5 3.8 - - - -
196B VAL* 4.0 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B SER* 3.2 31.6 + - - +
121B ALA 3.0 20.2 + - - -
123B MET* 3.4 16.3 - - + +
124B GLY* 3.4 17.9 - - - -
125B ALA* 4.2 0.7 - - - -
135B VAL* 3.7 19.1 - - + -
136B ASN 3.6 17.0 - - - -
137B GLY* 3.4 28.5 - - - -
138B SER* 1.3 72.0 + - - +
140B ASN* 1.3 62.3 + - - +
153B VAL* 3.5 30.5 - - + -
154B GLY 2.8 30.5 + - - +
169B PHE* 5.5 1.6 - + - -
193B ASN 4.0 1.0 - - - +
194B THR* 3.2 4.2 - - - -
195B LEU* 2.8 47.2 + - + +
197B VAL* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A ASN* 5.8 3.8 - - - +
119B SER* 2.6 26.0 + - - -
123B MET* 2.8 35.9 - - - +
138B SER 4.0 0.6 + - - +
139B TRP* 1.3 74.1 - - - +
141B TRP* 1.3 93.2 + - + +
142B SER 3.4 1.9 + - - -
181B VAL* 6.0 0.4 - - + -
193B ASN 3.8 0.2 - - - -
194B THR* 3.6 20.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B TRP* 3.6 33.7 - + - -
118B SER 4.2 3.7 - - - +
119B SER* 4.9 1.6 + - - -
123B MET* 5.5 0.2 - - + -
140B ASN* 1.3 101.8 - - - +
142B SER* 1.3 59.5 + - - +
143B SER* 3.3 9.8 + - - -
182B TRP* 3.6 31.8 - + - -
187B LEU* 4.1 15.5 - - + -
190B THR* 5.1 0.2 - - - -
192B SER* 3.4 38.4 + - - -
193B ASN 3.5 1.4 + - - -
364B ALA* 4.7 7.6 - - + -
367B VAL* 5.9 3.7 - - + +
368B HIS* 3.5 55.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 3.4 14.6 + - - -
118B SER 2.9 23.8 + - - -
119B SER* 4.5 2.0 - - - -
140B ASN 3.4 0.6 + - - -
141B TRP* 1.3 72.1 - - - +
143B SER* 1.3 63.4 + - - +
144B GLY 3.3 0.7 + - - -
145B CYS* 3.1 37.4 + - - +
191B GLY 3.4 4.3 - - - +
192B SER* 3.6 3.8 - - - -
193B ASN 2.9 17.3 + - - -
195B LEU* 3.5 23.1 - - - +
----------------------------------------------------------
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