Contacts of the strand formed by residues 128 - 135 (chain B) in PDB entry 4ZGY
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 ILE 128 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B VAL 3.3 3.6 - - - +
119B GLN* 3.3 1.9 - - - -
120B SER* 2.9 46.1 + - - +
122B LEU* 6.1 0.7 - - + -
126B LYS* 3.4 11.7 - - + +
127B ARG* 1.3 79.6 - - - +
129B ASN* 1.3 65.0 + - - +
130B TRP* 3.6 32.5 + - + +
149B PRO* 3.7 32.5 - - + -
150B GLU 3.3 24.0 - - - +
151B GLY 3.9 18.8 - - - +
152B SER* 3.9 5.6 - - - +
155B SER* 4.0 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B LEU* 5.4 3.6 - - - +
117B ASN* 5.4 7.3 - - + +
118B VAL 3.6 4.0 + - - +
119B GLN* 3.4 41.2 + - - +
127B ARG* 4.3 4.4 + - - +
128B ILE* 1.3 78.2 - - - +
130B TRP* 1.3 67.7 + - - +
131B ARG 4.2 0.7 + - - -
144B PRO* 6.0 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LEU 3.6 1.6 - - - +
117B ASN* 3.7 2.5 - - - -
118B VAL* 2.9 46.1 + - + +
120B SER* 4.9 1.6 - - - -
128B ILE* 3.6 26.1 - - + +
129B ASN* 1.3 77.2 - - - +
131B ARG* 1.3 60.7 + - - +
132B THR* 3.7 9.3 + - + -
141B ILE* 4.2 10.1 - - + -
142B GLU 4.2 13.7 - - - -
143B ILE* 4.7 3.8 - - + -
144B PRO* 3.9 25.8 - - + -
148B LEU* 3.9 19.5 - - + -
149B PRO* 4.6 4.0 - - + -
152B SER* 4.3 15.5 - - - -
155B SER* 2.7 28.8 + - - -
156B PHE* 3.5 34.3 - + - -
159B LEU* 3.5 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 4.5 19.7 - - + -
116B LEU 4.0 2.2 - - - +
117B ASN* 4.9 4.9 - - + +
129B ASN 4.2 1.2 + - - -
130B TRP* 1.3 72.7 - - - +
132B THR* 1.3 63.6 + - - +
133B VAL* 5.7 2.7 - - + -
140B TYR 4.1 0.2 - - - +
141B ILE* 4.2 0.5 - - - +
142B GLU* 2.9 60.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 3.7 4.0 - - - +
116B LEU* 2.9 53.2 + - - +
118B VAL* 3.9 11.9 - - + +
130B TRP* 4.1 14.6 - - + +
131B ARG* 1.3 79.5 - - - +
133B VAL* 1.3 68.9 + - - +
139B LEU* 3.4 21.9 - - + +
140B TYR 3.2 9.6 - - - -
141B ILE* 3.7 28.3 - - + -
159B LEU* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 5.4 7.4 - - - +
114B ARG 3.7 5.2 - - - +
115B ILE* 4.0 27.4 - - + -
131B ARG* 5.7 3.6 - - + -
132B THR* 1.3 79.8 - - - +
134B LEU* 1.3 61.5 + - - +
135B SER* 5.6 3.1 - - - -
138B SER 3.5 1.7 - - - +
139B LEU* 3.4 7.2 - - - -
140B TYR* 2.9 62.6 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
113B THR* 3.6 4.8 - - - +
114B ARG* 2.8 58.2 + - + +
116B LEU* 4.6 7.4 - - + +
133B VAL* 1.3 70.9 - - - +
135B SER* 1.3 62.3 + - - +
137B GLY* 4.4 9.2 - - - +
138B SER 3.4 27.6 - - - +
139B LEU* 4.0 14.5 - - + +
167B LEU* 4.2 37.7 - - + +
169B ALA* 5.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B THR* 3.7 26.0 - - - +
133B VAL* 3.7 4.6 + - - -
134B LEU* 1.3 75.4 - - - +
136B GLY* 1.3 68.9 + - - +
137B GLY 3.2 1.6 - - - -
138B SER* 2.9 26.3 + - - +
140B TYR* 3.7 21.3 + - - -
----------------------------------------------------------
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