Contacts of the strand formed by residues 94 - 98 (chain A) in PDB entry 2YVL
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 ARG 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LYS* 1.3 73.9 - - - +
95A VAL* 1.3 62.9 + - - +
115A GLU* 2.9 48.2 + - + +
117A TRP* 3.8 6.1 - - + +
158A ILE* 2.9 48.6 + - - +
159A PHE* 3.6 27.0 - - + -
160A HIS* 2.9 47.8 + - + +
161A ALA 3.5 3.1 + - - -
181A MET* 6.0 0.2 - - - -
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Residues in contact with VAL 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.8 2.9 - - + -
89A LEU* 3.8 25.1 - - + -
94A ARG* 1.3 75.6 - - - +
96A LEU* 1.3 74.0 + - - +
109A LEU* 4.3 14.4 - - + -
113A ALA* 3.7 24.5 - - + -
115A GLU 3.0 7.9 + - - -
116A VAL* 3.3 24.1 - - + +
117A TRP 2.9 24.9 + - - -
159A PHE* 3.6 4.8 - - - -
161A ALA* 3.4 23.3 - - + +
162A ALA* 4.2 4.3 - - - +
163A PHE 4.6 0.4 - - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL* 1.3 78.1 - - - +
97A GLU* 1.3 67.2 + - - +
98A PHE* 4.6 5.4 - - + -
117A TRP 3.6 2.2 - - - +
119A PHE* 3.2 38.1 - - + -
149A PHE* 3.8 30.7 - - + -
154A VAL* 5.2 0.4 - - + -
159A PHE* 3.4 24.6 - - + -
161A ALA 2.9 10.8 + - - +
162A ALA* 3.2 17.6 - - + -
163A PHE* 2.8 26.8 + - - +
176A VAL* 4.6 9.0 - - + -
179A SER* 4.1 21.5 - - - -
180A LEU* 5.9 0.4 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 1.3 76.6 - - - +
98A PHE* 1.3 69.4 + - - +
99A GLY 4.4 9.6 - - - +
100A THR* 3.9 5.6 - - - +
105A LEU* 3.5 21.1 - - + +
106A LEU* 3.4 35.6 + - - +
109A LEU* 3.8 24.5 - - + -
116A VAL* 4.4 3.8 - - + -
117A TRP 3.0 9.9 + - - +
118A THR* 2.6 35.3 + - - +
119A PHE* 3.0 25.8 + - - -
163A PHE* 3.4 11.0 - - + +
165A ASP* 6.4 0.7 - - + -
601A SAM 4.3 7.3 + - - +
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Residues in contact with PHE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A LEU* 4.6 6.5 - - + -
97A GLU* 1.3 79.8 - - - +
99A GLY* 1.3 60.4 + - - +
119A PHE* 3.4 24.7 - - + +
149A PHE* 3.4 52.3 - + + -
163A PHE 3.4 3.5 + - - +
164A VAL* 3.4 37.0 - - + +
165A ASP 2.8 27.1 + - - +
166A VAL* 3.8 15.0 - - + -
172A TYR* 3.8 28.5 - + + -
176A VAL* 3.7 17.7 - - + -
601A SAM 4.0 9.6 - - + -
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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