Contacts of the helix formed by residues 86 - 93 (chain D) in PDB entry 5NVL
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 GLU 86 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D PHE 4.1 0.2 + - - -
85D THR* 1.3 73.8 - - - +
87D GLU* 1.3 64.4 + - + +
89D GLN* 3.8 15.7 + - - +
90D ARG* 3.0 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D THR* 3.5 10.0 + - - +
86D GLU* 1.3 79.6 - - + +
88D GLU* 1.3 65.8 + - + +
90D ARG* 3.6 22.7 + - - +
91D ASN* 2.9 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C GLY 5.2 5.5 - - - +
146C ARG* 2.8 42.9 + - - +
79D LEU* 4.8 7.6 - - - +
82D VAL* 5.1 0.7 - - - +
83D PRO 4.0 0.7 - - - +
84D PHE* 3.6 7.0 - - + -
85D THR* 3.1 34.2 + - - +
87D GLU* 1.3 80.8 - - + +
89D GLN* 1.3 65.5 + - - +
91D ASN* 3.0 6.3 + - - +
92D PHE* 2.9 49.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 89 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A PRO* 4.5 0.2 - - - +
208A PRO* 3.9 31.5 - - + +
93B SER 3.2 25.9 + - - +
94B MET* 3.7 34.4 + - + +
84D PHE* 3.9 20.6 - - + +
85D THR 2.6 21.2 + - - +
86D GLU* 3.8 18.2 + - - +
88D GLU* 1.3 72.6 - - - +
90D ARG* 1.3 59.0 + - - +
92D PHE* 4.2 0.5 - - - +
93D SER* 2.6 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B MET* 6.0 1.8 - - - -
140C ARG* 4.7 4.8 + - - +
86D GLU 3.0 17.5 + - - +
87D GLU* 3.6 24.3 + - - +
89D GLN* 1.3 75.0 - - - +
91D ASN* 1.3 77.0 + - - +
92D PHE 3.2 1.0 + - - -
93D SER* 3.3 12.0 + - - -
94D MET* 3.8 14.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 91 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C ARG* 3.6 28.6 + - - +
141C LYS 4.0 17.0 + - - -
142C GLY* 4.3 10.8 + - - +
143C LEU* 3.4 25.0 - - + +
87D GLU* 2.9 31.9 + - - +
88D GLU* 3.0 7.7 + - - +
90D ARG* 1.3 92.3 + - - +
92D PHE* 1.3 59.0 + - + +
93D SER 3.8 0.2 + - - -
94D MET 4.8 0.2 + - - -
95D SER 3.6 19.1 - - - +
96D VAL* 4.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLN* 4.0 3.5 + - - -
142C GLY 3.8 10.3 - - - -
143C LEU* 3.5 42.4 - - + -
146C ARG* 3.6 44.0 - - + -
147C CYS* 4.4 9.2 - - - -
150C ASN* 6.3 0.9 - - - -
204C LEU 5.7 3.4 - - - -
205C ASN 5.4 4.7 - - - +
206C LEU* 5.1 11.7 - - + -
207C PRO* 3.8 19.9 - - - +
84D PHE* 3.9 25.6 - + + -
88D GLU* 2.9 40.7 + - + +
89D GLN 4.4 1.3 - - - +
91D ASN* 1.3 77.0 - - - +
93D SER* 1.3 63.7 + - - +
94D MET 3.7 0.4 - - - -
96D VAL* 4.2 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLN* 3.3 29.5 + - - +
90B ARG* 6.4 0.4 - - - -
93B SER* 3.3 29.2 + - - -
94B MET* 4.0 13.7 - - - -
207C PRO* 3.8 1.7 - - - +
84D PHE* 6.1 0.3 - - - -
89D GLN* 2.6 23.6 + - - +
90D ARG* 3.3 6.4 + - - -
92D PHE* 1.3 79.1 - - - +
94D MET* 1.3 67.5 + - - +
----------------------------------------------------------
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