Contacts of the strand formed by residues 111 - 116 (chain S) in PDB entry 1VYH
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 111 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107S HIS* 3.6 28.3 - - + -
110S PRO* 1.3 77.4 - - - +
112S THR* 1.3 59.5 + - - +
113S ARG 3.7 17.3 - - - +
114S VAL* 4.4 3.1 - - + -
125S SER* 4.2 3.1 - - - -
126S ALA 3.1 16.4 - - - +
127S SER* 4.1 0.2 - - - +
384S THR* 3.1 27.5 + - - +
385S SER* 4.6 0.4 - - - +
398S GLY* 4.5 2.0 - - - -
399S SER 4.2 15.8 + - - +
402S GLN 4.3 1.1 - - - -
403S THR 4.0 21.1 - - - +
404S VAL* 3.6 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110S PRO 4.1 0.7 + - - -
111S VAL* 1.3 74.9 - - - +
113S ARG* 1.3 83.3 + - - +
126S ALA* 2.7 11.6 + - - -
127S SER* 3.4 15.1 - - - -
128S GLU* 3.7 8.6 + - + +
153S VAL 2.8 25.3 + - - +
154S GLN* 3.1 43.9 + - + +
384S THR* 3.6 13.2 - - + +
385S SER* 3.4 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111S VAL* 3.7 5.0 - - - +
112S THR* 1.3 102.6 + - - +
114S VAL* 1.3 71.3 - - - +
115S ILE* 5.7 3.8 - - + -
125S SER* 3.3 4.7 - - - -
126S ALA* 3.0 31.0 + - + +
154S GLN* 2.6 29.7 + - - +
155S ASP* 2.9 28.8 + - - +
156S ILE* 4.7 19.2 - - + +
196S SER* 3.6 14.6 + - - -
238S ARG 5.4 1.2 + - - -
239S MET* 3.6 34.2 - - + +
241S ARG* 6.2 0.2 - - - +
342S ARG 6.0 0.9 + - - -
384S THR 5.1 1.6 - - - -
385S SER* 3.4 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111S VAL* 4.4 0.7 - - + -
113S ARG* 1.3 83.9 - - - +
115S ILE* 1.3 72.6 + - - +
123S MET* 3.7 29.2 - - + -
124S VAL 3.5 2.7 - - - -
385S SER* 3.4 35.4 + - - +
386S LEU* 4.1 13.7 + - - +
387S ASP* 3.8 11.8 - - - +
396S VAL* 3.9 23.8 - - + -
397S THR 3.9 0.7 - - - -
398S GLY* 3.4 15.0 - - - +
404S VAL* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113S ARG* 5.7 4.0 - - + -
114S VAL* 1.3 79.4 - - - +
116S PHE* 1.3 67.3 + - - +
123S MET* 3.1 8.5 - - - +
124S VAL* 2.7 57.4 + - + +
156S ILE* 3.4 46.9 - - + +
157S SER* 4.7 4.7 - - - -
158S PHE* 3.9 24.2 - - + +
241S ARG* 5.8 4.5 - - - +
387S ASP* 4.1 15.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 116 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115S ILE* 1.3 81.6 - - - +
117S HIS* 1.3 66.6 + - - +
118S PRO* 3.7 3.1 - - - +
122S VAL 4.3 0.9 - - - -
123S MET* 3.9 6.7 - - + -
137S TYR* 3.3 46.2 - + + -
158S PHE* 3.7 13.5 - - - +
387S ASP* 3.2 40.0 + - + +
388S PHE 3.6 5.8 - - - -
389S HIS* 3.2 48.9 - + + -
394S TYR* 3.9 25.4 - - + -
396S VAL* 3.4 20.0 - - + -
----------------------------------------------------------
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