Contacts of the strand formed by residues 133 - 139 (chain A) in PDB entry 4AB1
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 LEU 133 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PRO* 3.6 34.5 - - + -
125A ALA* 3.9 20.6 - - + +
131A ASN* 4.3 14.6 - - + +
132A ARG* 1.3 77.9 - - - +
134A PRO* 1.3 77.9 - - + +
162A ASN* 3.7 33.9 - - - +
164A VAL* 4.0 7.2 - - + -
209A GLY 2.8 17.5 + - - +
210A GLY* 3.3 2.9 - - - -
211A ASN* 2.6 25.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ARG 4.2 2.5 - - - +
133A LEU* 1.3 92.4 - - + +
135A VAL* 1.3 60.0 + - - +
162A ASN 4.0 6.5 - - - +
163A VAL* 3.5 27.8 - - + +
164A VAL 3.0 24.3 + - - -
211A ASN* 4.9 0.2 - - + -
214A SER* 3.8 17.9 - - - +
504A ALA* 4.5 12.6 - - + -
505A ARG* 4.0 37.5 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
133A LEU 3.7 11.0 - - - +
134A PRO* 1.3 75.0 - - - +
136A MET* 1.3 66.5 + - - +
137A VAL* 3.9 15.9 - - + -
164A VAL* 3.4 7.2 - - + +
166A VAL* 3.8 27.1 - - + -
201A VAL* 4.1 10.8 - - + -
205A ILE* 3.8 15.7 - - + -
210A GLY* 3.8 10.8 - - - -
211A ASN 3.7 26.0 - - - +
214A SER 2.9 11.7 + - - +
215A VAL* 3.4 6.4 - - + -
216A THR* 2.8 27.5 + - - -
504A ALA* 5.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 1.3 75.5 - - - +
137A VAL* 1.3 62.6 + - - +
138A TRP 3.7 0.7 + - - -
157A LEU* 4.4 12.1 - - + -
163A VAL* 4.3 26.0 - - + -
164A VAL 2.8 12.1 + - - +
165A VAL* 3.5 5.8 - - - +
166A VAL 2.9 26.3 + - - +
216A THR* 3.4 13.5 - - + +
218A PHE* 3.5 42.1 - - + -
244A ILE* 4.5 1.8 - - + -
500A TRP* 3.8 30.5 - - + +
501A ALA* 4.3 12.3 - - - -
504A ALA* 3.7 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.9 13.5 - - + -
136A MET* 1.3 73.6 - - - +
138A TRP* 1.3 60.3 + - - +
139A ILE* 3.9 3.5 + - + +
166A VAL* 3.4 13.0 - - + +
168A ILE* 3.7 36.1 - - + -
197A ALA* 5.8 0.4 - - + -
198A LEU* 4.0 24.5 - - + -
201A VAL* 4.2 10.8 - - + -
215A VAL* 3.8 24.2 - - + -
216A THR 2.8 12.1 + - - +
217A ILE* 3.4 7.5 - - + +
218A PHE* 2.9 28.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
136A MET 5.1 0.2 - - - +
137A VAL* 1.3 71.8 - - - +
139A ILE* 1.3 66.6 + - - +
140A HIS* 3.7 12.8 + - + +
141A GLY 5.2 0.4 - - - -
149A ALA* 5.8 0.9 - - - -
152A TYR* 3.4 46.4 - + + -
165A VAL* 5.1 0.9 - - + -
166A VAL 2.8 15.7 + - - +
167A THR* 4.1 15.0 - - + -
168A ILE* 3.2 29.2 + - - +
218A PHE* 3.3 60.2 - + + -
219A GLY* 3.6 10.8 - - - -
220A GLU* 3.5 25.4 - - + -
246A GLU* 3.7 12.3 - - - -
472A LEU* 3.4 34.5 - - + -
476A PHE* 3.4 20.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A VAL* 4.4 6.1 - - + +
138A TRP* 1.3 79.4 - - - +
140A HIS* 1.3 63.1 + - - +
168A ILE* 4.0 20.4 - - + -
170A TYR* 3.7 13.9 - - + -
194A GLN* 3.7 27.1 - - - +
198A LEU* 6.0 1.3 - - + -
217A ILE* 4.7 9.0 - - + -
218A PHE 2.7 15.3 + - - +
219A GLY* 3.1 18.9 - - - -
220A GLU 3.5 1.9 + - - -
223A GLY* 3.2 22.1 - - - +
226A SER* 3.9 5.4 - - - -
227A VAL* 4.1 17.5 - - + -
230A LEU* 3.7 30.3 - - + -
----------------------------------------------------------
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