Contacts of the strand formed by residues 107 - 114 (chain V) in PDB entry 5LN3
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 MET 107 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58V LEU* 3.5 22.3 - - - -
59V GLY 3.5 12.1 + - - +
60V GLU* 3.4 26.0 - - - +
61V PHE* 3.3 41.7 - - + +
96V LEU* 6.3 0.4 - - - -
106V GLU* 1.4 76.4 - - - +
108V VAL* 1.3 85.2 + - + +
109V VAL* 3.5 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 108 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V LEU* 4.1 27.1 - - + -
57V MET 3.2 9.4 - - - +
58V LEU* 4.2 8.8 - - + +
61V PHE* 4.7 2.9 - - - -
92V GLN* 6.1 2.2 - - - +
107V MET* 1.3 83.7 - - + +
109V VAL* 1.4 58.7 + - - +
110V GLY* 3.1 32.1 - - - +
133V PHE* 6.2 2.7 - - + -
137V SER* 5.3 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57V MET* 3.0 37.9 + - + +
58V LEU 4.4 5.2 - - - -
59V GLY 3.6 24.0 - - - +
60V GLU 3.8 3.6 - - - +
61V PHE* 3.4 38.7 - - + -
67V VAL* 4.3 14.6 - - + -
68V ARG 4.3 4.9 - - - +
69V VAL* 4.5 1.8 - - + -
107V MET* 3.5 21.9 + - + -
108V VAL* 1.4 70.9 - - - +
110V GLY* 1.4 61.0 + - - +
137V SER* 5.7 0.9 - - - -
139V ARG 4.0 0.2 - - - +
140V ALA* 3.4 16.7 - - - +
141V VAL* 3.8 5.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56V LEU* 4.0 1.2 - - - +
57V MET* 3.1 25.4 + - - -
108V VAL* 3.1 18.3 - - - +
109V VAL* 1.4 84.7 - - - +
111V TRP* 1.3 60.2 + - - +
133V PHE* 6.0 2.0 - - - -
137V SER* 5.9 0.4 - - - -
140V ALA* 3.7 14.8 - - - -
141V VAL* 3.7 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 111 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54V MET* 4.2 16.2 - - + -
55V GLY 3.6 12.8 - - - +
56V LEU* 4.3 2.9 - - + -
57V MET* 3.4 8.7 - - - +
82V VAL* 4.9 5.8 - - + -
110V GLY* 1.3 76.0 - - - +
112V TYR* 1.3 71.5 + - - +
113V HIS* 3.6 31.4 - + + -
126V ASP* 4.1 6.5 - - + -
129V THR* 3.5 29.4 - - + -
130V GLN* 3.7 49.2 - - + +
133V PHE* 3.2 47.0 - + + +
140V ALA* 5.0 4.0 - - + +
141V VAL 3.0 27.3 + - - +
142V ALA* 3.4 13.6 - - + +
143V VAL 3.3 11.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 112 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V MET* 4.1 30.5 - - + -
44V HIS* 4.6 12.9 - + + +
53V VAL* 4.6 11.0 - - + -
54V MET* 3.0 34.7 - - - +
55V GLY* 3.2 40.9 + - - +
56V LEU 3.7 11.2 - - - -
57V MET* 3.7 15.3 - - + -
72V VAL* 3.8 21.9 - - + +
73V PHE 3.5 19.6 + - - -
74V ALA* 3.8 8.3 + - - +
111V TRP* 1.3 77.5 - - - +
113V HIS* 1.3 63.7 - - - +
114V SER* 5.3 2.5 - - - -
143V VAL* 3.1 22.4 - - + +
145V VAL* 6.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 113 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52V GLU* 3.6 11.5 + - - +
53V VAL 3.5 8.5 - - - +
54V MET* 4.2 3.4 - - + +
82V VAL* 4.3 8.5 - - + +
111V TRP* 3.6 33.9 - + + -
112V TYR* 1.3 75.0 - - - +
114V SER* 1.4 78.3 + - - +
115V HIS* 3.1 37.8 + + - -
122V LEU* 4.2 8.0 - - + +
126V ASP* 2.9 34.4 + - + -
130V GLN* 5.8 0.7 - - - -
142V ALA* 5.9 1.7 - - + +
143V VAL 3.2 15.1 + - - +
144V VAL* 3.3 33.9 - - + +
145V VAL* 4.0 2.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45V GLY* 5.0 5.0 - - - -
51V MET 4.9 1.3 - - - -
52V GLU* 3.4 17.2 - - - +
53V VAL* 2.9 47.3 + - - +
112V TYR* 5.3 2.9 - - - -
113V HIS* 1.4 92.1 + - - +
115V HIS* 1.3 63.3 + - - +
116V PRO* 3.9 8.6 - - - +
144V VAL* 4.4 0.4 - - - -
145V VAL* 3.9 20.4 - - - +
147V PRO* 5.0 6.8 - - - +
----------------------------------------------------------
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