Contacts of the strand formed by residues 122 - 127 (chain H) 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 122 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117H HIS* 3.1 48.9 + - + +
120H PHE* 2.7 18.2 + - + +
121H SER* 1.3 73.9 - - - +
123H MET* 1.3 62.2 + - - +
124H VAL* 5.2 0.7 - - + -
134H VAL* 3.4 25.8 - - + -
135H TRP 3.1 19.1 - - - +
136H ASP* 3.2 13.2 - - + +
137H TYR* 3.4 6.8 - - - -
143H GLU* 4.1 14.8 - - - +
179H PHE* 4.5 9.6 - - + -
369L ASN* 6.5 0.2 - - + -
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Residues in contact with MET 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H LEU* 4.5 4.5 - - + -
114H VAL* 4.1 1.8 - - + -
115H ILE 3.1 20.0 - - - +
116H PHE* 3.4 18.2 - - + -
117H HIS 4.4 1.3 - - - +
122H VAL* 1.3 77.5 - - - +
124H VAL* 1.3 72.3 + - - +
125H SER* 4.3 1.6 - - - -
134H VAL* 3.7 2.4 - - - -
135H TRP* 2.5 83.5 + - + +
137H TYR* 3.9 13.1 - - + -
396H VAL* 4.1 28.7 - - + -
404H VAL* 3.7 25.6 - - + -
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H VAL* 3.5 2.8 - - - -
115H ILE* 2.8 42.6 + - + +
122H VAL* 5.2 1.3 - - + -
123H MET* 1.3 83.9 - - - +
125H SER* 1.3 61.8 + - - +
132H ILE* 3.5 30.1 - - + -
133H LYS 3.5 4.7 - - - +
134H VAL* 4.3 9.0 - - + -
156H ILE* 3.9 16.8 - - + +
158H PHE* 3.5 31.6 - - + -
165H LEU* 4.3 6.1 - - + -
179H PHE* 4.1 15.5 - - + -
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Residues in contact with SER 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H HIS* 2.3 35.6 + - - -
111H VAL* 4.1 2.5 - - - -
113H ARG 3.4 9.6 - - - -
114H VAL* 4.8 1.1 - - - -
123H MET* 4.3 2.5 - - - -
124H VAL* 1.3 75.2 - - - +
126H ALA* 1.3 59.7 + - - +
132H ILE* 3.4 5.9 - - - +
133H LYS 2.9 28.5 + - - -
135H TRP* 3.3 14.6 + - - -
156H ILE* 4.1 3.6 - - - -
404H VAL* 3.8 24.5 - - - -
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Residues in contact with ALA 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H VAL* 3.1 9.6 - - - +
112H THR* 2.7 22.7 + - - -
113H ARG* 3.0 19.0 + - + +
125H SER* 1.3 74.1 - - - +
127H SER* 1.3 62.1 + - - +
131H THR 3.8 4.9 - - - -
132H ILE* 4.6 0.7 - - + +
153H VAL* 3.6 27.4 - - + +
155H ASP 5.1 1.1 - - - +
156H ILE* 3.2 25.8 - - + +
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Residues in contact with SER 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107H HIS* 3.2 27.1 - - - -
109H SER 3.1 9.9 + - - -
110H PRO 2.8 18.8 + - - -
111H VAL* 3.9 1.6 - - - -
112H THR* 3.3 10.5 + - - -
126H ALA* 1.3 79.3 - - - +
128H GLU* 1.3 69.8 + - - +
129H ASP* 2.8 25.4 + - - +
130H ALA* 3.9 2.6 - - - -
131H THR 3.4 6.3 + - - -
153H VAL* 2.8 25.1 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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