Contacts of the strand formed by residues 129 - 139 (chain A) in PDB entry 2RFQ
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 129 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A VAL* 3.7 3.1 - - - +
126A VAL* 2.9 29.0 + - - +
127A ASP 3.3 1.2 + - - -
128A GLY* 1.3 81.2 - - - +
130A TYR* 1.3 77.6 + - - -
198A PHE* 4.1 1.1 - - - -
199A VAL 3.3 9.9 - - - -
201A THR* 3.5 16.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLY* 4.2 5.4 - - - -
124A GLN 3.1 17.3 - - - +
125A VAL* 4.1 12.3 - - + -
126A VAL* 3.7 6.7 - - - +
129A GLY* 1.3 88.3 - - - -
131A THR* 1.3 61.3 + - - +
132A VAL* 3.9 17.2 + - + -
154A VAL* 3.6 39.3 - - + +
164A VAL* 5.8 0.3 - - - +
166A PHE* 4.1 6.3 - + + -
197A VAL 3.4 0.5 - - - +
198A PHE* 3.3 5.8 - - - -
199A VAL* 2.8 39.7 + - - +
201A THR* 4.3 15.0 - - - +
204A VAL* 3.5 44.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA 3.8 1.2 - - - +
123A GLY* 3.3 0.9 - - - -
124A GLN* 2.8 44.6 + - - +
126A VAL* 3.4 23.6 - - - +
130A TYR* 1.3 71.0 + - - +
132A VAL* 1.3 64.0 + - - +
133A ASN* 4.1 11.4 + - - +
196A ASP* 3.2 40.2 - - - +
197A VAL 3.4 3.8 - - - +
198A PHE* 4.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA 3.3 10.5 - - - +
123A GLY* 4.0 2.2 - - - -
130A TYR* 4.1 2.9 - - + -
131A THR* 1.3 78.4 - - - +
133A ASN* 1.3 65.2 + - - +
136A TRP* 3.7 28.9 - - + -
166A PHE* 3.7 31.4 - - + -
168A ILE* 4.2 6.7 - - + -
194A VAL* 3.6 15.8 - - + +
196A ASP 3.3 7.3 + - - -
197A VAL 2.8 31.8 + - - +
199A VAL* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLY* 3.1 2.1 - - - -
122A ALA* 2.9 31.4 + - - +
131A THR* 4.1 12.5 + - - +
132A VAL* 1.3 78.1 + - - +
134A GLY* 1.3 59.2 + - - +
136A TRP* 4.0 4.0 - - - -
194A VAL 3.5 4.0 - - - +
195A GLU* 3.6 6.8 - - - +
196A ASP* 2.8 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MSE 3.4 11.4 - - - -
121A GLY* 3.7 0.7 - - - -
133A ASN* 1.3 75.8 - - - +
135A ALA* 1.3 62.0 + - - +
136A TRP* 3.5 17.8 - - - -
193A VAL* 3.6 3.8 - - - +
194A VAL 2.9 32.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MSE 3.0 23.7 + - - +
134A GLY* 1.3 74.1 - - - +
136A TRP* 1.3 60.2 + - - +
137A ALA* 3.4 6.2 + - - +
191A THR* 3.9 16.1 - - + +
192A VAL 3.5 5.2 - - - -
193A VAL* 4.3 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 3.3 33.0 + - - +
118A ALA 3.2 19.1 + - - -
120A MSE 3.4 11.8 - - + +
121A GLY* 3.4 31.6 - - - -
132A VAL* 3.7 24.7 - - + -
133A ASN 4.0 0.2 - - - -
134A GLY* 3.5 26.0 - - - -
135A ALA* 1.3 70.7 - - - +
137A ALA* 1.3 63.2 + - - +
139A SER* 4.5 0.5 - - - -
150A LEU* 3.6 44.2 - - + -
151A GLY 2.8 31.2 + - - +
166A PHE* 4.7 4.0 - + - -
190A ASN 3.9 1.6 - - - +
191A THR* 3.3 3.6 - - - -
192A VAL* 2.8 42.5 + - + +
194A VAL* 4.0 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER* 2.7 26.2 + - - -
120A MSE 3.3 17.5 - - - +
135A ALA 3.4 6.2 + - - +
136A TRP* 1.3 72.7 - - - +
138A TRP* 1.3 91.6 + - + +
139A SER 3.3 1.0 + - - -
178A VAL* 5.9 0.9 - - + -
190A ASN 3.9 0.2 - - - -
191A THR* 3.5 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A SER 4.2 4.1 - - - +
116A SER* 5.0 2.0 + - - +
120A MSE 4.4 10.7 - - + -
137A ALA* 1.3 104.2 - - + +
139A SER* 1.3 59.2 + - - +
140A SER* 3.1 11.7 + - - -
179A TRP* 3.5 37.2 - + - -
181A VAL* 5.0 4.3 - - + -
189A SER* 3.5 25.1 + - - -
190A ASN 3.5 1.2 + - - -
364A VAL* 4.2 10.5 - - + -
343B ALA* 3.6 41.3 - - + -
344B THR* 6.0 0.4 - - - -
346B LEU* 4.1 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 3.0 26.5 + - - -
115A SER 2.8 25.5 + - - -
116A SER* 4.6 1.8 - - - -
136A TRP 4.5 4.9 - - - -
137A ALA 3.3 0.6 - - - -
138A TRP* 1.3 73.1 - - - +
140A SER* 1.3 64.6 + - - +
141A GLY 3.3 0.5 + - - -
142A CYS* 3.1 28.0 + - - +
150A LEU* 5.6 0.3 - - - +
188A GLY 3.6 4.0 - - - +
189A SER* 3.6 2.8 - - - -
190A ASN 3.0 16.2 + - - -
192A VAL* 3.9 15.1 - - - +
----------------------------------------------------------
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