Contacts of the strand formed by residues 119 - 125 (chain A) in PDB entry 5WVD
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 119 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 5.2 3.0 - - - -
50A LEU* 5.8 0.2 - - - +
62A LYS* 4.6 3.6 - - - +
79A ILE* 3.8 20.3 - - + +
80A ILE 3.4 13.9 - - - +
81A GLU* 4.3 7.4 - - - -
82A LYS* 3.8 9.7 - - - +
115A GLU* 3.7 1.4 - - - -
116A ASP* 2.8 38.2 + - - +
118A THR* 1.3 85.6 + - - +
120A PHE* 1.3 61.4 + - - +
121A TYR* 2.6 41.0 + - + +
81B GLU* 2.9 43.8 + - - -
118B THR* 4.1 16.4 + - - -
119B ARG* 3.5 43.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS 4.5 0.7 - - - -
79A ILE* 3.4 6.9 - - - +
80A ILE* 2.8 44.0 + - + +
82A LYS* 3.7 33.0 - - + -
87A SER* 3.9 19.1 - - - -
88A ARG* 3.8 38.6 - - + -
91A VAL* 3.7 27.1 - - + -
92A PHE* 5.3 2.7 - - + -
113A PHE* 3.6 28.3 - + + -
114A PHE 3.8 1.1 - - - -
115A GLU* 3.7 31.2 - - + -
119A ARG* 1.3 72.8 - - - +
121A TYR* 1.3 64.3 + - - +
122A LEU* 4.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 3.6 50.1 - + + +
77A VAL* 4.2 3.1 - - + -
78A LYS 3.7 2.9 - - - -
79A ILE* 3.7 31.9 - - + -
112A GLU 3.8 1.0 - - - +
113A PHE* 3.5 7.8 - - - -
114A PHE* 2.7 71.9 + + + +
116A ASP* 2.5 44.3 + - + -
119A ARG* 2.6 36.6 + - + -
120A PHE* 1.3 74.3 - - - +
122A LEU* 1.3 63.2 + - - +
123A VAL* 3.8 3.0 - - + +
118B THR* 4.3 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL* 3.8 2.6 - - - +
78A LYS* 2.8 45.0 + - + +
80A ILE* 3.8 23.6 - - + -
91A VAL* 3.8 13.2 - - + -
94A GLU* 4.7 10.8 - - + -
95A VAL* 3.8 24.5 - - + -
98A LEU* 4.6 9.4 - - + -
110A LEU* 3.9 9.2 - - + -
112A GLU 3.8 3.1 - - - -
113A PHE* 3.7 22.2 - - + -
121A TYR* 1.3 73.9 - - - +
123A VAL* 1.3 60.9 + - - +
124A PHE* 3.3 37.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A PHE* 4.7 3.8 - - + -
47A MET* 6.3 0.2 - - + -
48A TYR* 3.4 52.9 - - + +
75A TYR* 3.8 26.0 - - + -
77A VAL* 3.9 23.8 - - + -
110A LEU* 3.5 2.8 - - - +
111A ILE* 2.7 35.5 + - + -
112A GLU* 2.8 27.5 + - + +
114A PHE* 5.7 2.9 - - + +
121A TYR* 4.7 4.9 - - + +
122A LEU* 1.3 69.2 - - - +
124A PHE* 1.3 54.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 3.4 12.8 - - - +
76A ALA 2.9 31.7 + - - +
78A LYS* 4.0 12.8 - - + -
98A LEU* 3.7 30.7 - - + -
108A LEU* 3.7 40.4 - - + -
109A GLU 3.4 15.0 - - - -
110A LEU* 3.7 12.6 - - + -
111A ILE* 4.0 3.6 - - - -
122A LEU* 3.3 47.7 + - + -
123A VAL* 1.3 74.1 - - - +
125A GLU* 1.3 68.0 + - - +
190A CYS* 6.5 0.4 - - - -
191A ASP* 5.7 8.3 - - + -
230A PHE* 6.3 0.7 - + - -
402A 7UX 3.6 22.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A TYR* 4.5 5.4 - - + -
76A ALA* 4.1 1.0 - - - +
107A ILE 4.1 0.2 - - - +
108A LEU* 3.6 14.9 - - + +
109A GLU* 2.9 48.5 + - + +
111A ILE* 3.9 12.9 - - + +
124A PHE* 1.3 77.2 - - - +
126A LYS* 1.3 62.0 + - - +
127A LEU* 4.0 9.6 - - - +
188A LYS* 2.8 38.9 + - - +
402A 7UX 3.5 17.3 - - - -
----------------------------------------------------------
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