Contacts of the strand formed by residues 133 - 143 (chain A) in PDB entry 4YCV
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
----------------------------------------------------------
109A THR* 4.1 21.5 - - + -
110A ILE* 4.3 19.5 - - + -
115A PHE* 3.8 23.8 - - + -
119A TYR* 3.8 23.8 - - + +
131A THR* 4.5 7.0 - - - +
132A ILE* 1.3 80.0 - - - +
134A ASN* 1.3 68.9 + - - +
135A ILE 4.0 0.4 - - - -
192A ILE 3.5 1.0 - - - +
193A VAL* 3.5 0.2 - - - -
194A GLY 2.9 36.3 + - - +
196A PRO* 3.7 33.7 - - + -
206A ILE* 4.8 5.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.5 15.7 - - + -
107A GLU* 3.4 28.0 + - - +
108A ARG* 3.7 6.2 - - - +
109A THR* 3.1 36.2 + - - +
110A ILE 3.8 4.9 + - - -
132A ILE* 4.4 4.9 - - - +
133A LEU* 1.3 83.2 - - - +
135A ILE* 1.3 59.3 + - - +
192A ILE 3.1 4.5 - - - -
193A VAL* 3.8 26.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 4.8 0.2 - - - -
110A ILE* 3.6 27.8 - - + +
112A ILE* 4.0 15.5 - - + +
115A PHE* 3.6 39.5 - - + -
133A LEU* 4.0 1.2 - - + -
134A ASN* 1.3 73.4 - - - +
136A THR* 1.3 71.0 + - - +
154A LEU* 4.0 18.8 - - + -
161A ILE* 3.9 13.5 - - + -
192A ILE* 2.8 36.9 + - + +
206A ILE* 3.5 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A PHE* 3.4 35.2 - - + -
108A ARG* 3.0 22.4 + - + +
112A ILE* 3.7 22.3 - - - +
135A ILE* 1.3 79.3 - - - +
137A GLY* 1.3 59.2 + - - +
154A LEU* 4.0 6.3 - - - +
156A GLY* 5.5 0.2 - - - -
190A VAL 3.2 9.2 - - - -
191A GLY* 3.7 1.6 - - - -
214A LEU* 3.6 15.7 - - + -
351B TYR* 3.0 35.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
112A ILE* 4.6 0.2 - - - -
136A THR* 1.3 79.5 - - - +
138A ARG* 1.3 59.7 + - - -
154A LEU* 3.4 14.7 - - - +
155A VAL 3.4 11.7 - - - -
156A GLY* 5.1 2.5 - - - -
189A ILE* 3.2 5.5 - - - +
190A VAL 2.9 29.5 + - - +
351B TYR* 3.8 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLY* 1.3 74.2 - - - -
139A ILE* 1.3 64.4 + - - +
140A MET* 3.3 9.7 + - - -
154A LEU* 3.5 4.2 - - - +
155A VAL* 2.9 43.8 + - + +
187A GLY* 3.2 41.4 + - - +
188A ASP 3.4 2.0 - - - -
189A ILE* 3.5 34.0 - - + +
217A CYS* 4.9 0.8 - - - +
221A LEU* 4.7 0.6 - - - +
242A LEU* 3.4 37.3 - - + +
315B ILE 4.6 2.4 + - - -
316B VAL* 2.5 37.9 + - - +
318B GLY* 4.9 2.2 - - - +
545B TYR 3.0 26.5 + - - -
546B GLY* 3.9 3.2 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
138A ARG* 1.3 70.9 - - - +
140A MET* 1.3 57.0 + - - +
141A ARG 3.5 26.0 - - - +
142A VAL* 4.6 1.8 - - + -
152A PHE* 3.7 37.2 - - + -
153A ASP 3.7 2.7 - - - +
154A LEU* 3.8 13.9 - - + -
163A VAL* 4.9 3.6 - - + -
184A ILE* 3.9 20.4 - - + -
185A ARG 4.2 9.9 - - - +
186A ARG* 3.4 4.9 - - - -
187A GLY* 2.4 35.0 + - - -
188A ASP 2.8 22.7 + - - +
190A VAL* 3.7 25.6 - - + -
192A ILE* 5.4 0.9 - - + -
211A THR* 6.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 4.0 13.9 - - - +
139A ILE* 1.3 79.1 - - - +
141A ARG* 1.3 61.4 + - - +
153A ASP* 2.9 10.0 + - + +
155A VAL* 3.5 43.5 - - + -
160A LYS* 5.4 4.3 - - - +
186A ARG* 3.0 52.0 + - - +
187A GLY 4.8 0.2 - - - -
221A LEU* 3.7 32.8 - - + -
242A LEU* 4.8 18.6 - - + +
243A ILE* 5.0 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 3.5 8.1 - - - +
140A MET* 1.3 79.2 - - - +
142A VAL* 1.3 68.5 + - - +
143A SER* 2.9 29.3 + - - +
151A PHE 4.8 0.2 - - - -
152A PHE* 3.2 6.0 - - - -
153A ASP* 2.9 56.6 + - + +
160A LYS* 6.1 0.4 - - - +
186A ARG* 4.9 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ILE* 4.6 4.7 - - + -
141A ARG* 1.3 81.1 - - - +
143A SER* 1.3 73.8 + - - +
144A ALA* 6.4 0.2 - - + -
151A PHE 3.9 3.1 - - - -
152A PHE* 3.6 27.4 - - + -
184A ILE* 4.5 10.8 - - + +
185A ARG* 5.2 2.0 - - - -
186A ARG* 4.2 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ARG* 2.9 30.4 + - - +
142A VAL* 1.3 84.2 + - - +
144A ALA* 1.3 64.1 + - - +
150A ARG* 4.1 8.1 - - - +
151A PHE* 3.1 44.6 + - - +
152A PHE* 5.4 0.5 - - - -
----------------------------------------------------------
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