Contacts of the strand formed by residues 119 - 123 (chain J) in PDB entry 6H25
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 HIS 119 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J PRO* 6.1 2.1 - - - +
47J ALA* 3.6 27.2 + - + +
48J LEU* 4.7 6.2 - - - +
49J GLU* 4.0 13.1 - - + +
86J ARG* 2.9 48.6 + - + +
87J ASN* 3.3 22.7 - - - +
88J VAL 3.4 10.2 + - - +
116J GLN* 3.2 32.5 + - + +
117J GLU* 3.2 21.3 + - - -
118J LYS* 1.3 68.8 - - - +
120J PHE* 1.3 66.0 + - - +
121J TYR 4.3 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J PRO* 3.6 23.5 - - - +
47J ALA 4.9 1.1 - - - -
48J LEU* 4.4 0.9 - - - -
73J LEU* 6.4 2.0 - - + -
80J LEU* 4.3 11.2 - - + -
85J ILE 5.0 0.2 - - - -
86J ARG 4.6 3.4 - - - -
88J VAL* 3.3 42.8 - - + +
90J VAL* 4.3 21.3 - - + -
109J ILE* 5.2 7.0 - - + -
112J VAL* 3.6 24.5 - - + -
113J THR* 4.3 34.4 + - + +
115J ASN 5.3 0.8 + - - -
118J LYS* 3.1 44.6 + - + +
119J HIS* 1.3 82.4 - - - +
121J TYR* 1.3 59.8 + - - +
122J THR* 4.1 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 4.6 9.3 + - - -
29J ILE* 4.8 3.5 - - - +
30J GLY* 2.7 26.8 + - - -
31J CYS 3.4 24.5 - - - -
32J GLY* 3.5 16.6 + - - -
43J HIS* 5.9 3.7 + + + -
46J PRO* 3.6 26.2 - - + +
47J ALA 5.0 0.2 - - - +
48J LEU* 2.8 32.1 - - + +
88J VAL 3.5 6.1 + - - -
89J ILE* 3.5 7.9 - - + +
90J VAL* 2.9 24.5 + - - +
120J PHE* 1.3 72.7 - - - +
122J THR* 1.3 81.3 + - - +
123J PHE* 3.8 16.5 - + + -
124J THR 5.7 0.2 + - - -
156J TYR* 4.0 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B GLN* 3.2 42.6 + - - +
90J VAL* 3.3 18.8 - - + +
92J GLN* 5.1 9.6 - - + -
95J LEU* 4.6 21.7 - - + +
113J THR* 3.7 25.0 + - - +
120J PHE* 4.1 1.3 + - - +
121J TYR* 1.3 87.4 + - - +
123J PHE* 1.3 66.6 + - - +
124J THR* 4.1 1.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J ILE* 4.0 10.5 - - + -
30J GLY 3.8 15.7 - - - -
31J CYS* 4.5 1.3 - - - -
89J ILE* 4.4 6.5 - - + -
90J VAL 2.8 15.5 + - - +
91J LEU* 3.7 24.8 - - + -
92J GLN* 3.1 23.3 + - - +
121J TYR* 3.8 14.4 - + + -
122J THR* 1.3 73.9 - - - +
124J THR* 1.3 60.3 + - - +
125J ASN* 2.9 33.3 + - + -
128J HIS* 4.2 16.2 - + - -
131J THR* 4.6 8.5 - - + -
152J ALA* 5.3 2.9 - - + -
155J TRP* 3.7 30.1 - + - -
156J TYR* 3.2 31.6 - + - +
----------------------------------------------------------
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