Contacts of the strand formed by residues 111 - 116 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D HIS* 4.3 9.2 - - + -
109D SER 4.3 2.7 - - - +
110D PRO* 1.3 77.4 - - - +
112D THR* 1.3 58.1 + - - +
113D ARG 4.2 6.1 - - - +
114D VAL* 4.7 4.9 - - + -
125D SER* 4.1 22.7 - - - +
126D ALA 2.9 22.4 - - - +
127D SER* 4.1 0.7 - - - +
384D THR* 3.1 26.8 + - - +
385D SER* 5.0 0.4 - - - -
398D GLY 4.3 1.6 - - - -
399D SER 2.7 20.4 + - - +
402D GLN* 4.0 6.3 - - - -
403D THR 3.3 34.3 - - - +
404D VAL* 4.1 9.4 - - + -
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D PRO 4.0 0.3 + - - -
111D VAL* 1.3 75.1 - - - +
113D ARG* 1.3 77.5 + - - +
126D ALA* 2.7 9.5 + - - -
127D SER* 3.1 18.4 - - - -
128D GLU* 3.7 8.5 + - + +
153D VAL 2.9 27.9 + - - +
154D GLN* 3.7 32.3 - - + +
384D THR* 3.3 16.6 - - + +
385D SER* 3.2 12.6 + - - -
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Residues in contact with ARG 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D VAL* 3.8 0.7 - - - +
112D THR* 1.3 90.5 + - - +
114D VAL* 1.3 72.8 + - - +
115D ILE* 5.1 2.0 - - + -
125D SER* 3.4 4.9 - - - -
126D ALA* 3.0 27.5 + - + +
154D GLN* 3.0 32.7 + - - +
155D ASP* 3.1 28.3 + - - +
156D ILE* 3.7 21.4 - - + +
196D SER* 3.4 20.6 + - - -
238D ARG 5.0 2.4 + - - -
239D MET* 3.2 36.1 - - - +
241D ARG* 4.0 5.0 - - - +
342D ARG 5.9 0.2 + - - -
384D THR* 6.1 0.9 - - - -
385D SER* 3.5 15.9 + - - -
386D LEU 6.1 0.2 - - - -
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Residues in contact with VAL 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D VAL* 4.7 6.1 - - + -
113D ARG* 1.3 84.0 - - - +
115D ILE* 1.3 70.6 + - - +
123D MET* 3.1 36.1 - - + -
124D VAL 3.5 2.5 - - - +
125D SER* 4.2 2.7 - - - -
385D SER* 3.9 11.3 + - - +
386D LEU 4.1 7.3 - - - +
387D ASP* 3.8 16.9 - - - +
396D VAL* 3.7 25.4 - - + +
397D THR* 4.0 3.8 - - - +
398D GLY* 3.6 35.0 - - - +
404D VAL* 4.0 5.8 - - + -
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Residues in contact with ILE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D ARG* 5.1 4.0 - - + -
114D VAL* 1.3 84.9 - - - +
116D PHE* 1.3 62.0 + - - +
123D MET* 3.0 8.5 - - - +
124D VAL* 2.7 48.8 + - + +
156D ILE* 3.1 51.4 - - + +
157D SER* 3.8 9.0 - - - -
158D PHE* 3.6 35.4 - - + +
387D ASP* 4.5 5.4 - - - -
396D VAL* 4.9 0.4 - - - +
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Residues in contact with PHE 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D ILE* 1.3 77.3 - - - +
117D HIS* 1.3 66.7 + - - +
118D PRO* 3.7 2.9 - - - +
122D VAL 4.3 0.2 - - - -
123D MET* 3.5 17.3 - - + -
137D TYR* 3.4 46.9 - + + -
158D PHE* 3.7 11.1 - - - +
387D ASP* 3.3 33.8 + - - +
388D PHE 4.0 0.2 - - - -
389D HIS* 3.7 32.1 - + + -
394D TYR* 3.6 37.5 - - + -
395D VAL 4.4 0.7 - - - -
396D VAL* 3.3 31.2 - - + -
406D VAL* 5.4 0.2 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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