Contacts of the strand formed by residues 109 - 117 (chain A) in PDB entry 3NMV
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 VAL 109 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A VAL* 5.6 0.7 - - + -
25A TYR* 3.7 43.5 - - + -
51A TRP* 3.5 5.3 - - - -
102A PHE* 3.8 25.5 - - + -
103A VAL* 3.3 3.3 - - - -
104A ASP* 2.8 31.8 + - + -
107A HIS* 3.8 15.7 - - + +
108A ARG* 1.3 83.5 - - - +
110A LEU* 1.3 63.1 + - - +
127A VAL* 4.0 15.3 - - + -
128A THR 3.3 9.2 - - - +
129A SER* 3.9 14.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TRP* 3.9 8.0 - - + -
54A ILE* 3.6 38.4 - - + +
55A ARG* 4.0 20.9 - - - +
57A PHE* 5.0 8.1 - - + -
83A ARG* 6.0 0.4 - - - +
100A LEU* 3.7 28.3 - - + -
102A PHE 3.4 4.5 - - - +
103A VAL* 4.1 9.9 - - + -
109A VAL* 1.3 76.7 - - - +
111A SER* 1.3 73.9 + - - +
112A PHE* 4.2 17.5 - - + -
126A SER* 4.1 0.7 + - - +
127A VAL* 3.5 0.5 - - - -
128A THR* 2.9 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.5 6.4 - - - +
101A GLU* 2.9 35.9 + - - +
102A PHE* 2.8 25.6 + - - +
110A LEU* 1.3 79.7 - - - +
112A PHE* 1.3 62.9 + - - +
126A SER 3.1 13.9 + - - -
127A VAL* 3.9 20.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A PHE* 4.2 10.1 - - + -
63A TYR* 5.8 1.6 - - - -
64A LYS* 3.7 15.3 - - - -
83A ARG* 3.7 19.5 - - - -
98A GLU* 3.7 30.7 - - + -
99A ARG 3.1 19.1 - - - +
101A GLU* 4.1 4.3 - - - -
110A LEU* 4.2 16.8 - - + -
111A SER* 1.3 75.7 + - - +
113A ARG* 1.3 67.3 + - - +
114A VAL* 4.6 1.6 - - + -
124A TYR* 4.5 8.7 - + - -
125A LYS* 3.4 3.7 - - - +
126A SER* 2.9 61.3 + - - +
128A THR* 5.7 1.3 - - - -
147A GLU* 4.7 2.7 - - - -
900A PYV 3.5 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 3.3 2.1 - - - -
99A ARG* 2.7 34.7 + - + +
101A GLU* 3.3 39.5 + - + +
112A PHE* 1.3 81.1 - - - +
114A VAL* 1.3 67.4 + - - +
115A VAL* 3.9 14.6 + - + +
123A ASN* 3.5 27.7 - - - +
124A TYR 3.2 12.1 - - - +
125A LYS* 3.8 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A SER* 4.0 4.0 - - - +
97A THR 3.3 7.2 - - - +
98A GLU* 4.2 12.8 - - + +
112A PHE* 4.6 2.0 - - + -
113A ARG* 1.3 77.4 + - - +
115A VAL* 1.3 63.0 + - - +
116A GLY 3.2 13.5 - - - +
119A HIS* 3.2 38.6 - - + +
121A LEU 4.6 0.4 - - - +
122A LYS* 5.2 3.8 + - - -
123A ASN* 4.6 13.8 + - - +
124A TYR* 2.9 50.5 + - + +
900A PYV 3.9 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A VAL* 4.8 7.2 - - + -
97A THR* 2.7 37.2 + - + +
98A GLU* 4.6 1.1 - - - +
99A ARG* 4.5 15.5 - - + +
113A ARG* 4.1 22.9 - - + +
114A VAL* 1.3 77.4 - - - +
116A GLY* 1.3 57.2 + - - +
122A LYS* 5.7 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 3.1 35.1 + - - -
114A VAL* 3.2 4.8 - - - +
115A VAL* 1.3 81.1 - - - +
117A GLY* 1.3 55.4 + - - -
119A HIS* 2.6 25.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 3.4 25.6 - - - -
96A SER 5.1 0.2 - - - -
97A THR* 4.9 0.4 + - - -
116A GLY* 1.3 74.3 - - - -
118A GLU* 1.3 58.5 + - - -
119A HIS* 3.4 13.1 + - - -
120A ARG 5.2 0.5 + - - -
----------------------------------------------------------
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