Contacts of the strand formed by residues 95 - 99 (chain H) in PDB entry 2NN6
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 ARG 95 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ARG* 5.0 7.3 - - - +
91H VAL* 2.8 3.0 - - - +
92H GLN* 2.6 72.5 + - + +
94H LYS* 1.3 83.2 - - + +
96H TRP* 1.3 58.7 + - - +
97H LYS* 4.6 19.0 - - + +
107H VAL* 3.6 27.4 - - + +
108H LEU 3.6 5.4 - - - +
109H LEU* 3.6 25.6 - - + +
110H LEU* 4.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 96 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91H VAL* 3.0 38.4 - - + -
95H ARG* 1.3 74.3 - - - +
97H LYS* 1.3 61.5 + - - +
98H VAL* 5.5 0.9 - - + -
107H VAL* 3.1 3.5 - - - +
108H LEU* 2.6 84.7 + - + +
109H LEU 3.6 2.2 - - - -
110H LEU* 3.1 42.4 - - + -
111H SER 5.0 0.2 - - - -
112H SER 5.0 0.7 - - - -
113H MET* 3.9 18.6 - - + -
131H MET* 2.9 47.6 + - + +
134H PHE* 3.3 25.6 - + - -
135H LEU* 3.5 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 4.6 13.2 + - - -
61B ARG* 3.7 32.7 - - - +
88H ILE* 3.4 3.6 - - - +
89H THR* 2.4 37.2 + - - +
90H GLU* 2.9 30.2 + - + +
91H VAL* 3.3 8.9 - - - +
92H GLN* 4.1 33.4 - - + +
95H ARG* 4.6 15.4 - - + +
96H TRP* 1.3 74.7 - - - +
98H VAL* 1.3 57.8 + - - +
105H ASP* 5.2 1.8 - - - +
107H VAL* 3.4 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86H GLY* 4.8 6.7 - - - -
87H ARG 3.4 8.3 - - - +
88H ILE* 3.4 35.0 - - + +
89H THR* 3.6 3.1 - - - -
97H LYS* 1.3 77.6 - - - +
99H GLU* 1.3 56.8 + - - +
105H ASP* 2.6 23.0 - - - +
106H SER* 2.5 62.2 + - - +
108H LEU* 3.9 21.8 - - + -
135H LEU* 5.4 1.1 - - + -
141H ILE* 4.9 7.6 - - + -
156H LEU* 3.7 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ARG* 4.0 24.1 + - - +
5E THR* 6.0 1.8 - - + +
86H GLY* 3.4 1.6 - - - -
87H ARG* 2.6 41.7 + - + +
89H THR* 3.9 12.1 - - + -
98H VAL* 1.3 73.9 - - - +
100H THR* 1.3 105.0 + - - +
101H ASN* 3.4 14.7 + - - +
105H ASP* 4.1 11.9 - - - +
202H PHE* 4.4 4.4 - - - -
----------------------------------------------------------
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