Contacts of the strand formed by residues 94 - 98 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89D LEU* 4.6 0.5 - - - +
92D GLU 5.0 3.2 + - - +
93D LYS* 1.3 75.9 - - - +
95D VAL* 1.3 60.6 + - - +
115D GLU* 3.3 35.7 - - + +
117D TRP* 6.1 0.7 - - - +
158D ILE* 2.7 49.1 + - - +
159D PHE* 3.8 15.9 - - + -
160D HIS* 2.9 62.3 + - - +
161D ALA 3.5 1.9 + - - -
181D MET* 3.8 9.5 - - - +
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Residues in contact with VAL 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D LEU* 4.6 3.8 - - + -
89D LEU* 3.9 26.5 - - + -
94D ARG* 1.3 75.6 - - - +
96D LEU* 1.3 71.9 + - - +
109D LEU* 4.3 20.9 - - + -
113D ALA* 3.8 12.8 - - + -
115D GLU 2.9 9.1 + - - +
116D VAL* 3.4 33.1 - - + +
117D TRP 3.0 25.3 + - - -
159D PHE* 3.6 6.3 - - - -
161D ALA* 3.4 19.7 - - + +
162D ALA* 4.3 2.2 - - - +
163D PHE 4.7 0.2 - - - +
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Residues in contact with LEU 96 (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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95D VAL* 1.3 75.6 - - - +
97D GLU* 1.3 63.3 + - - +
98D PHE* 3.7 31.9 - - + -
117D TRP 3.6 5.8 - - - +
119D PHE* 4.5 9.6 - - + -
149D PHE* 3.9 19.3 - - + -
154D VAL* 4.1 6.5 - - + -
159D PHE* 3.6 20.1 - - + -
161D ALA 3.0 10.9 + - - +
162D ALA* 3.2 18.9 - - + -
163D PHE 2.9 26.7 + - - +
164D VAL* 5.5 0.2 - - + -
176D VAL* 5.1 4.3 - - + +
179D SER* 3.5 33.9 - - - +
180D LEU* 5.5 0.4 - - + -
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Residues in contact with GLU 97 (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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95D VAL 4.2 0.2 + - - -
96D LEU* 1.3 74.6 - - - +
98D PHE* 1.3 68.4 + - - +
99D GLY 4.2 9.5 - - - +
100D THR* 3.9 5.4 - - - +
105D LEU* 3.4 26.6 - - + +
106D LEU* 3.6 23.8 + - - +
109D LEU* 3.8 26.7 - - + -
116D VAL* 4.6 3.8 - - + -
117D TRP 3.0 9.1 + - - +
118D THR* 2.4 38.8 - - + +
119D PHE* 3.0 27.0 + - - -
163D PHE* 3.5 11.4 - - + +
165D ASP* 6.1 1.1 - - + +
603D SAM 4.1 8.9 + - - +
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Residues in contact with PHE 98 (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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96D LEU* 3.7 11.2 - - + -
97D GLU* 1.3 78.8 - - - +
99D GLY* 1.3 61.4 + - - +
119D PHE* 3.4 24.0 - - + +
149D PHE* 3.5 58.1 - + + -
163D PHE 3.4 1.8 + - - -
164D VAL* 3.4 28.9 - - + -
165D ASP* 2.8 28.0 + - - +
166D VAL* 3.6 23.3 - - + -
172D TYR* 3.8 27.4 - + + -
176D VAL* 3.8 13.7 - - + -
603D SAM 4.1 8.7 - + + -
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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