Contacts of the strand formed by residues 111 - 117 (chain A) in PDB entry 5NVL
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 SER 111 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 4.0 8.7 + - - -
65A SER 3.3 8.1 - - - -
66A ARG* 3.4 16.3 - - - +
107A LEU* 3.8 29.8 - - - +
108A THR 2.9 22.0 + - - -
109A GLY 2.9 9.0 + - - -
110A HIS* 1.3 71.4 - - - +
112A ASP* 1.3 74.0 + - - +
173A VAL* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.4 10.2 - - - -
65A SER* 2.9 48.0 + - - +
80A GLN* 4.7 8.5 + - - +
107A LEU* 4.9 2.7 - - - -
110A HIS* 4.6 5.4 + - - +
111A SER* 1.3 91.0 - - - +
113A PHE* 1.3 64.8 + - - +
114A HIS* 3.7 18.1 + - + +
170A VAL* 4.5 0.7 - - + -
171A VAL 3.3 9.6 - - - +
172A SER* 2.7 20.2 + - - +
174A ARG* 2.6 29.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 5.3 0.7 - - + -
63A TRP 3.5 7.2 - - - +
64A TYR* 3.6 22.9 - + + -
101A MET* 3.6 33.4 - - + -
102A VAL 3.2 28.0 - - - -
104A PRO* 4.1 24.5 - - + -
107A LEU* 3.9 28.0 - - + +
112A ASP* 1.3 80.1 - - - +
114A HIS* 1.3 60.8 + - - +
148A TRP* 3.9 19.1 - - + -
170A VAL* 3.3 7.3 - - - +
171A VAL* 2.9 42.4 + - + +
70B ILE* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR 4.2 0.4 - - - -
62A PHE* 3.3 7.8 - - - -
63A TRP* 2.8 60.8 + - + +
64A TYR 4.1 0.9 - - - -
65A SER* 3.2 27.2 + - - -
82A ILE* 3.9 19.7 - - + +
112A ASP* 3.7 18.5 - - + +
113A PHE* 1.3 77.9 - - - +
115A LEU* 1.3 61.7 + - - +
116A PHE* 3.9 16.2 - - + -
122A PRO* 3.9 18.5 + - + +
148A TRP* 4.4 1.6 - - - -
169A ALA 3.5 4.7 - - - -
170A VAL* 3.5 21.7 - - + +
183A TRP* 5.8 0.9 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.9 8.5 - - + -
61A THR 3.4 17.9 - - - +
62A PHE* 3.8 25.6 - - + -
88A PHE* 3.7 36.1 - - + -
114A HIS* 1.3 74.0 - - - +
116A PHE* 1.3 59.3 + - - +
148A TRP* 3.9 15.5 - - + -
152A ILE* 3.6 33.0 - - + -
155A MET* 3.6 18.6 - - + +
156A LEU* 4.5 7.4 - - + -
168A GLY* 3.0 3.5 - - - -
169A ALA 2.8 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A TYR* 3.3 7.1 - - - -
61A THR* 2.7 38.7 + - - +
63A TRP* 4.6 6.1 - - - +
114A HIS* 3.9 2.9 - - + -
115A LEU* 1.3 83.2 - - - +
117A LYS* 1.3 60.6 + - - +
120A ILE* 3.7 35.9 - - + +
121A LYS 4.7 0.2 - - - -
122A PRO* 3.7 28.0 - - + -
167A CYS* 3.4 18.4 - - + -
168A GLY* 3.8 6.3 - - - -
169A ALA 3.6 6.5 - - - -
170A VAL* 3.4 25.4 - - + -
183A TRP* 3.4 58.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.5 55.9 - - + -
59A ASN 3.4 7.9 - - - +
60A TYR* 3.8 22.8 - - + -
61A THR* 4.7 1.2 + - - -
116A PHE* 1.3 75.1 - - - +
118A GLU* 1.3 70.0 + - - +
119A GLY 3.3 0.3 + - - -
120A ILE* 3.0 39.8 + - + +
163A GLY 5.0 0.2 + - - -
164A GLU* 3.1 23.4 + - - +
166A ILE* 2.7 36.3 + - - +
167A CYS 3.0 13.8 + - - +
185A LYS* 4.4 5.5 - - - +
----------------------------------------------------------
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