Contacts of the strand formed by residues 90 - 95 (chain A) in PDB entry 4NTX
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 ALA 90 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A PRO* 1.3 75.5 - - - +
91A VAL* 1.3 62.7 + - - +
92A THR 4.1 0.7 - - - -
197A THR* 3.9 7.9 - - + -
198A PHE 3.5 8.3 - - - +
199A ASN 3.7 14.8 - - - +
200A ALA* 4.5 1.8 - - - -
249A GLN 3.8 0.2 - - - +
250A ILE* 3.5 4.3 - - - -
251A HIS* 2.8 60.3 + - + +
253A GLN* 3.7 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PHE* 4.1 25.6 - - + -
89A PRO* 4.4 3.4 - - + +
90A ALA* 1.3 78.5 - - - +
92A THR* 1.3 63.7 + - - +
93A PHE* 4.1 6.3 + - + +
185A PHE* 5.2 2.1 - - + -
196A TYR 3.5 1.6 - - - +
197A THR* 3.3 1.1 - - - -
198A PHE* 2.6 48.4 + - + +
219A LEU* 4.3 10.5 - - + -
221A ILE* 6.1 2.7 - - + -
248A VAL* 4.0 15.3 - - + -
249A GLN 3.6 2.9 - - - +
250A ILE* 4.6 7.4 - - + -
407A LEU* 5.3 2.9 - - + -
409A ILE* 3.8 34.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 1.3 72.8 - - - +
93A PHE* 1.3 67.6 + - - +
188A VAL* 3.9 16.4 - - + -
190A THR* 5.0 1.8 - - + -
195A CYS* 4.5 4.7 - - + -
196A TYR 3.2 6.7 - - - +
197A THR* 2.9 23.7 + - - +
248A VAL* 3.3 5.5 - - - +
249A GLN 2.8 35.3 + - - -
251A HIS* 2.7 30.1 + - - -
257A PRO* 4.0 19.9 - - + +
259A ILE* 3.4 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 5.2 6.1 - - + -
92A THR* 1.3 75.2 - - - +
94A CYS* 1.3 74.6 + - - +
166A ILE* 3.6 24.5 - - + -
169A MET* 3.9 27.4 - - + -
185A PHE* 3.7 28.5 - + - -
195A CYS* 3.2 4.2 - - - +
196A TYR* 2.9 50.2 + + + -
221A ILE* 4.6 11.4 - - + -
223A LEU* 3.8 34.1 - - + -
246A ILE* 4.3 9.4 - - + -
247A LYS 3.2 11.9 - - - +
248A VAL* 4.1 15.3 - - + -
259A ILE* 4.1 0.4 - - - -
407A LEU* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 1.3 80.5 - - - +
95A ASN* 1.3 69.9 + - - +
190A THR* 3.5 11.2 - - - -
192A TYR* 3.8 15.7 - - + -
194A LYS 5.1 0.2 - - - -
195A CYS* 2.0 50.0 - - - +
196A TYR* 6.1 0.2 - - - -
246A ILE* 3.2 6.6 - - - +
247A LYS* 3.0 33.0 + - + +
259A ILE* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.6 3.8 - - - -
94A CYS* 1.3 81.6 - - - +
96A LEU* 1.3 73.6 + - - +
97A ASN 3.1 20.0 + - - +
164A HIS* 3.5 33.4 + - + -
169A MET* 3.6 21.2 - - + +
192A TYR* 4.4 10.6 - - - +
194A LYS 5.2 4.2 + - - +
225A ILE* 2.9 31.1 + - - +
230A TYR* 2.8 27.3 + - - -
245A GLY 3.5 6.3 - - - +
246A ILE* 4.2 4.9 - - - +
----------------------------------------------------------
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