Contacts of the strand formed by residues 132 - 142 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A VAL* 3.6 3.1 - - - +
129A VAL* 2.8 29.6 + - - +
130A ASP 3.4 1.4 + - - -
131A GLY* 1.3 79.4 - - - +
133A TYR* 1.3 71.2 + - - -
201A PHE* 3.9 2.0 - - - -
202A VAL 3.3 12.6 - - - -
204A ARG* 3.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLY* 4.2 5.2 - - - -
127A VAL 3.3 6.5 - - - +
128A VAL* 4.0 19.5 - - + -
129A VAL* 3.8 6.3 - - - +
132A GLY* 1.3 77.6 - - - -
134A LEU* 1.3 59.9 + - - +
135A VAL* 4.1 8.1 - - + -
157A VAL* 3.6 29.4 - - + +
169A PHE* 3.7 28.5 - + + -
200A VAL 3.4 0.9 - - - +
201A PHE* 3.4 6.3 - - - -
202A VAL* 2.8 42.8 + - + +
203A PRO 4.4 0.4 - - - -
204A ARG* 3.8 37.9 + - + +
207A PHE* 3.6 40.1 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 3.8 1.4 - - - +
126A GLY* 3.4 0.5 - - - -
127A VAL* 2.7 44.4 + - + +
129A VAL* 3.9 23.7 - - + +
133A TYR* 1.3 73.0 - - - +
135A VAL* 1.3 58.5 + - - +
136A ASN* 4.2 7.2 + - - +
199A ASP* 3.5 53.2 - - + +
200A VAL 3.5 6.5 - - - +
201A PHE* 4.1 7.6 - - + +
161B GLY* 6.2 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 3.3 10.3 - - - +
126A GLY* 3.8 10.8 - - - -
133A TYR* 4.1 4.3 - - + -
134A LEU* 1.3 77.1 - - - +
136A ASN* 1.3 65.0 + - - +
139A TRP* 3.8 22.0 - - + -
153A VAL* 4.5 4.5 - - + -
169A PHE* 3.6 32.1 - - + -
171A ILE* 4.2 8.5 - - + -
197A VAL* 3.7 19.7 - - + +
199A ASP 3.2 7.6 + - - -
200A VAL 2.8 35.1 + - - +
202A VAL* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A GLY* 3.1 2.6 - - - -
125A ALA 3.1 30.4 + - - +
127A VAL* 6.4 0.2 - - - +
134A LEU* 4.2 12.7 + - - +
135A VAL* 1.3 81.4 + - - +
137A GLY* 1.3 58.9 + - - +
139A TRP* 3.7 5.1 - - - -
197A VAL 3.5 3.2 - - - +
198A LYS* 3.2 9.4 - - - +
199A ASP* 2.7 44.2 + - - +
160B ASP* 3.5 29.0 + - - +
161B GLY* 4.1 13.8 - - - +
162B ARG* 4.5 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A MET 3.5 9.2 - - - -
124A GLY* 3.8 1.1 - - - -
136A ASN* 1.3 75.6 - - - +
138A SER* 1.3 61.7 + - - -
139A TRP* 3.4 16.5 - - - -
196A VAL* 3.8 2.8 - - - +
197A VAL 3.0 32.4 + - - +
162B ARG* 4.5 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A MET* 3.1 25.7 + - - +
137A GLY* 1.3 75.3 - - - -
139A TRP* 1.3 60.1 + - - +
140A ASN* 4.1 0.5 + - - +
194A THR* 3.6 19.2 - - - +
195A LEU 3.4 4.7 - - - -
196A VAL* 4.1 14.1 - - - +
162B ARG* 3.4 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 3.1 36.7 + - - +
121A ALA 3.0 15.3 + - - -
123A MET* 3.2 13.7 - - + +
124A GLY* 3.3 33.9 - - - -
125A ALA* 5.2 0.2 - - - -
135A VAL* 3.8 16.2 - - + -
136A ASN 3.7 6.1 - - - -
137A GLY* 3.4 36.1 - - - -
138A SER* 1.3 72.0 + - - +
140A ASN* 1.3 60.9 + - - +
153A VAL* 3.5 31.6 - - + -
154A GLY 2.8 28.7 + - - +
169A PHE* 5.7 2.0 - + - -
194A THR* 3.3 3.4 - - - -
195A LEU* 2.7 49.6 + - + +
197A VAL* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A SER* 2.8 19.8 + - - -
123A MET* 3.0 30.9 - - - +
138A SER 4.1 0.8 + - - +
139A TRP* 1.3 72.9 - - - +
141A TRP* 1.3 87.7 + - + +
142A SER 3.3 3.4 + - - -
181A VAL* 5.9 0.9 - - + -
193A ASN 4.1 0.4 - - - -
194A THR* 3.3 20.2 - - + +
382B ASN* 5.9 3.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A TRP* 3.8 28.7 - + - -
118A SER 4.3 3.5 - - - +
119A SER* 4.9 1.7 - - - -
123A MET* 5.7 0.4 - - + -
140A ASN* 1.3 97.6 - - + +
142A SER* 1.3 60.2 + - - +
143A SER* 3.2 11.4 + - - -
182A TRP* 3.7 33.7 - + - -
187A LEU* 4.2 16.4 - - + -
192A SER* 3.4 36.6 + - - -
193A ASN 3.6 1.2 + - - -
364A ALA* 4.3 10.1 - - + -
367A VAL* 5.1 8.3 - - + +
368A HIS* 3.6 52.7 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.4 23.6 + - - -
118A SER 2.8 25.0 + - - -
119A SER* 4.3 3.4 - - - -
140A ASN 3.3 0.4 - - - -
141A TRP* 1.3 74.2 - - - +
143A SER* 1.3 63.3 + - - +
144A GLY 3.4 0.7 + - - -
145A CYS* 3.2 24.3 + - - +
191A GLY 3.5 3.5 - - - +
192A SER* 3.5 3.2 - - - -
193A ASN 3.0 16.2 + - - -
195A LEU* 3.6 23.5 - - - +
----------------------------------------------------------
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