Contacts of the strand formed by residues 108 - 113 (chain D) in PDB entry 3RHW
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 108 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ASP* 4.5 1.9 - - - +
151C TYR* 3.3 13.0 - - - -
152C ALA* 3.8 10.7 - - - +
100D LYS* 5.2 4.9 - - + +
101D HIS 5.9 0.2 - - - +
106D PRO* 3.0 27.5 + - + +
107D ASN* 1.3 82.9 - - - +
109D LEU* 1.3 64.1 + - - +
110D ILE* 5.6 5.2 - - + -
120D TYR* 4.8 13.9 - - + +
121D SER 3.2 7.9 - - - +
122D VAL* 3.9 20.0 - - + -
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Residues in contact with LEU 109 (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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151C TYR* 3.9 20.9 - - + +
152C ALA* 3.5 28.7 - - + +
197C THR* 4.8 6.3 - - + -
200C TYR* 3.6 24.5 - - - +
78D ILE* 4.6 9.2 - - + -
108D VAL* 1.3 77.7 - - - +
110D ILE* 1.3 77.7 + - - +
111D ARG* 3.9 36.1 - - + +
119D LEU* 3.6 5.2 - - + +
120D TYR* 3.4 2.1 - - - -
121D SER* 2.9 42.9 + - - +
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Residues in contact with ILE 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D ILE* 3.8 6.6 - - - +
79D LEU* 2.9 67.7 + - + +
85D ILE* 4.6 4.5 - - + -
87D MET* 3.8 30.5 - - + -
108D VAL* 5.6 6.0 - - + +
109D LEU* 1.3 82.3 - - - +
111D ARG* 1.3 67.8 + - - +
112D ILE* 4.6 3.1 - - + -
118D VAL* 4.2 16.2 - - + -
119D LEU 3.2 7.9 - - - +
120D TYR* 3.6 18.2 - - + -
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Residues in contact with ARG 111 (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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152C ALA 4.4 6.5 + - - -
154C THR* 4.8 9.9 - - - -
197C THR* 2.8 37.1 + - - +
200C TYR* 3.2 18.6 + - - -
76D PHE* 3.5 52.9 - - + -
77D VAL 3.9 3.1 - - - -
78D ILE* 4.7 5.5 - - + +
109D LEU* 3.9 28.2 - - + +
110D ILE* 1.3 77.3 - - - +
112D ILE* 1.3 62.3 + - - +
113D HIS* 3.8 12.7 + - + -
117D THR 3.6 0.9 - - - +
118D VAL* 3.2 9.7 - - - +
119D LEU* 2.8 54.9 + - + +
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Residues in contact with ILE 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D LEU* 4.4 12.3 - - + -
9D LEU* 4.4 6.5 - - + -
10D PHE* 4.6 2.0 - - + -
64D LEU* 3.5 48.0 - - + +
66D TYR* 3.1 16.7 - - + -
76D PHE* 4.1 0.4 - - - -
77D VAL* 3.1 28.0 + - + +
79D LEU* 3.6 26.2 - - + -
85D ILE* 3.2 34.1 - - + -
110D ILE* 4.6 2.0 - - + -
111D ARG* 1.3 77.0 - - - +
113D HIS* 1.3 64.8 + - - +
116D GLY* 5.1 0.7 - - - -
117D THR 3.8 2.5 - - - +
118D VAL* 4.6 5.4 - - + +
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Residues in contact with HIS 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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66D TYR* 3.6 2.9 - - - -
75D ASP* 3.6 25.6 - - - +
76D PHE* 3.7 25.5 - + + +
111D ARG* 4.3 21.3 + - + -
112D ILE* 1.3 79.2 - - - +
114D ASN* 1.3 68.9 + - - +
115D ASP* 3.2 16.4 - - - +
116D GLY* 2.9 15.8 + - - -
117D THR* 2.8 35.9 + - + +
119D LEU* 4.5 13.7 + - + -
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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
------------------------------------------------------------
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