Contacts of the strand formed by residues 122 - 127 (chain B) in PDB entry 3NVN
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 122 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PRO* 3.6 2.8 - - - +
112B TYR* 2.8 63.7 + - + +
113B ARG* 3.4 39.0 - - - +
120B GLY 3.7 4.2 + - - +
121B GLY* 1.3 85.3 - - - +
123B LEU* 1.3 61.3 + - - +
136B VAL* 3.9 17.9 - - + -
137B ARG 3.4 8.5 - - - +
138B PRO* 4.4 4.3 - - + -
139B LEU* 3.9 5.2 - - - +
147B LEU* 4.1 17.3 - - + -
148B ARG* 4.7 9.6 - - - +
211B GLU* 4.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B PHE* 4.1 31.0 - - + -
65B LEU* 4.3 5.4 - - + -
109B LEU* 4.2 14.8 - - + -
110B LEU 3.6 23.1 - - - +
111B PRO* 3.8 17.5 - - + -
112B TYR* 4.4 1.8 - - - -
122B LEU* 1.3 77.4 - - - +
124B LEU* 1.3 61.5 + - - +
125B THR* 3.6 25.7 + - + -
135B GLU 3.4 2.8 - - - +
136B VAL* 3.5 1.2 - - - -
137B ARG* 2.7 51.3 + - + +
138B PRO 5.3 2.0 - - - +
139B LEU* 3.8 17.7 - - + -
142B LEU* 4.5 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.6 13.8 - - + +
109B LEU* 3.4 6.4 - - - -
110B LEU* 2.9 39.0 + - + +
112B TYR* 3.6 17.3 - - + +
123B LEU* 1.3 72.5 - - - +
125B THR* 1.3 61.4 + - - +
126B GLY 4.1 0.4 - - - -
134B CYS* 4.1 16.6 - - - -
135B GLU 3.6 0.9 - - - +
136B VAL* 3.5 32.5 - - + -
166B VAL* 3.5 31.9 - - + -
177B LEU* 3.7 26.9 - - + -
210B THR* 4.7 6.3 - - + -
215B LEU* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B LEU* 3.9 15.3 - - + -
108B LEU 3.5 4.5 - - - -
109B LEU* 4.1 5.8 - - + -
123B LEU* 3.6 28.7 - - + -
124B LEU* 1.3 75.4 - - - +
126B GLY* 1.3 59.7 + - - +
127B TRP* 3.3 18.5 - - - -
134B CYS* 3.3 2.5 - - - -
135B GLU* 3.0 47.7 + - - +
137B ARG* 2.6 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B SER* 3.9 1.7 + - - -
107B LYS* 3.1 18.0 + - - -
108B LEU* 2.8 32.4 + - - +
125B THR* 1.3 72.6 - - - +
127B TRP* 1.3 73.7 + - - -
133B ALA 3.4 7.9 - - - -
134B CYS* 3.8 10.9 - - - -
154B VAL* 4.4 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B ALA* 5.2 3.3 - - + +
62B GLY 4.9 4.9 + - - -
63B SER 5.0 3.4 - - - -
64B CYS 5.1 2.2 + - - -
65B LEU* 4.3 19.7 - - + -
79B LEU* 3.4 29.4 - - + -
81B ARG* 3.5 31.1 - - + +
105B PHE* 2.9 29.6 - - + -
106B SER* 3.4 22.3 - - - +
107B LYS* 4.1 2.7 - - - +
109B LEU* 6.4 0.4 - - + -
125B THR* 3.3 33.4 - - + -
126B GLY* 1.3 75.9 - - - -
128B THR* 1.3 62.4 + - - +
129B PHE* 3.3 33.3 - + + +
132B GLY* 3.0 23.0 - - - -
133B ALA 2.9 10.1 + - - +
135B GLU* 2.7 30.1 - - - -
137B ARG* 4.0 1.3 - - - -
154B VAL* 3.3 14.5 - - - +
----------------------------------------------------------
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