Contacts of the strand formed by residues 136 - 146 (chain A) in PDB entry 1ZMD
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 THR 136 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 4.2 18.7 + - - +
128A THR* 3.3 24.3 - - - +
129A ALA 3.7 2.8 + - - -
130A THR* 4.4 4.7 + - - -
131A LYS* 5.8 2.4 - - - +
134A GLY 3.7 4.2 + - - -
135A GLY* 1.3 74.4 - - - -
137A GLN* 1.3 62.8 + - - +
138A VAL* 4.7 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 2.8 41.7 + - - +
5A ILE* 3.5 26.2 - - + +
115A VAL* 4.0 31.2 - - + -
127A VAL 3.9 0.5 - - - +
128A THR* 3.4 3.2 - - - -
129A ALA* 2.9 40.8 + - - +
131A LYS* 5.2 9.4 - - - -
136A THR* 1.3 75.3 + - - +
138A VAL* 1.3 90.1 + - - +
139A ILE* 4.4 9.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN 5.0 0.2 + - - -
4A PRO* 4.5 16.1 - - + +
5A ILE 2.9 13.8 + - - -
126A GLN* 3.3 38.4 - - + +
127A VAL 3.6 2.7 - - - +
128A THR* 3.9 18.4 - - + +
136A THR* 4.7 9.0 - - + +
137A GLN* 1.3 96.5 + - - +
139A ILE* 1.3 67.3 + - - +
140A ASP* 4.2 10.5 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
5A ILE* 3.2 14.6 - - + +
7A ALA* 4.4 3.6 - - + -
10A THR* 3.3 24.7 - - + +
33A VAL* 3.4 39.3 - - + -
35A ILE* 3.6 27.1 - - + -
115A VAL* 3.9 14.6 - - + -
126A GLN* 3.3 4.7 - - - -
127A VAL* 2.8 45.7 + - + +
129A ALA* 5.4 0.4 - - + -
137A GLN* 4.4 11.0 - - + +
138A VAL* 1.3 80.6 - - - +
140A ASP* 1.3 69.5 + - - +
141A THR* 3.6 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.1 19.2 - - - +
5A ILE 2.9 9.6 + - - +
6A ASP* 3.2 12.5 - - + +
7A ALA 2.9 24.3 + - - +
125A ASN* 3.4 7.1 - - + +
126A GLN* 3.1 29.9 - - - +
138A VAL* 4.7 3.6 - - - +
139A ILE* 1.3 73.4 - - - +
141A THR* 1.3 58.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 141 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA 3.1 11.0 + - - -
8A ASP 3.6 2.6 + - - -
9A VAL 3.7 0.2 + - - -
10A THR* 3.1 30.2 + - - +
125A ASN* 2.9 40.6 + - - +
126A GLN 4.3 0.4 - - - +
127A VAL* 4.4 2.9 - - + -
139A ILE* 4.1 8.1 - - - +
140A ASP* 1.3 76.9 - - - +
142A LYS* 1.3 63.0 + - - +
143A ASN 2.7 29.1 + - - +
144A ILE* 3.6 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ALA 3.1 10.8 + - - +
8A ASP* 3.4 34.7 + - + +
125A ASN* 3.3 8.7 + - - +
141A THR* 1.3 73.0 + - - +
143A ASN* 1.3 69.3 + - - +
314A ASN* 2.9 28.8 + - - +
409E GLN* 5.9 3.4 - - - +
2017E SO4 5.8 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 143 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP* 2.8 25.9 + - - +
9A VAL* 4.3 8.2 - - - +
10A THR 3.0 13.2 + - - -
30A PHE* 5.2 6.7 - - - -
141A THR* 2.7 24.4 + - - +
142A LYS* 1.3 90.4 - - - +
144A ILE* 1.3 65.1 - - - +
145A LEU 4.3 0.2 - - - -
314A ASN* 3.2 19.2 - - - +
316A TYR* 3.7 18.3 + - + -
342A MET* 4.2 24.4 - - + +
414E ARG* 5.4 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 144 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR 3.4 5.2 - - - +
12A ILE* 3.9 27.8 - - + -
121A ILE* 3.8 32.8 - - + -
123A GLY 4.0 3.1 - - - +
124A LYS 3.8 22.7 - - - +
126A GLN 4.2 2.0 - - - +
127A VAL* 3.7 19.5 - - + -
141A THR* 3.6 16.4 - - + -
143A ASN* 1.3 82.1 - - - +
145A LEU* 1.3 58.1 + - - +
146A ILE* 4.3 4.5 - - + -
314A ASN 3.0 5.3 + - - -
315A ILE* 3.4 17.6 - - + -
316A TYR* 2.7 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 4.7 2.5 - - + -
10A THR 2.9 13.3 + - - +
11A VAL* 3.5 20.7 - - + +
12A ILE* 2.9 27.5 + - - +
21A ALA* 3.5 32.3 - - + -
144A ILE* 1.3 73.2 - - - +
146A ILE* 1.3 67.2 + - - +
147A ALA* 3.4 1.5 + - + -
316A TYR* 3.8 21.8 - - + -
318A ILE* 3.7 34.8 - - + -
335A GLY 4.9 1.3 - - - +
338A CYS* 4.1 5.4 - - - -
339A VAL* 4.3 13.7 - - + -
342A MET* 4.3 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 146 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ILE* 4.3 6.7 - - + -
121A ILE* 4.0 21.3 - - + -
144A ILE* 4.3 6.3 - - + -
145A LEU* 1.3 74.7 - - - +
147A ALA* 1.3 60.6 + - - +
148A THR* 3.5 25.6 - - + +
287A LEU* 3.5 18.4 - - + -
289A LEU* 4.0 12.8 - - + -
294A ILE* 5.2 0.2 - - + -
302A ILE* 3.8 26.5 - - + -
310A THR* 4.6 5.8 - - + -
315A ILE* 3.8 18.6 - - + -
316A TYR 2.7 22.7 + - - +
317A ALA* 3.2 4.2 - - + +
318A ILE 3.1 27.0 + - - +
321A VAL* 3.9 3.0 - - + +
----------------------------------------------------------
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