Contacts of the strand formed by residues 95 - 100 (chain B) 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 GLU 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 2.8 26.5 + - + +
93B PRO 3.3 0.2 - - - -
94B ASN* 1.3 76.7 + - - +
96B LYS* 1.3 59.7 + - - +
97B GLN 3.3 35.2 + - - +
98B ALA* 3.5 19.7 + - + +
126B LEU* 3.9 4.3 - - + -
127B VAL 4.5 0.2 - - - +
128B LEU* 3.7 13.7 - - + -
52C GLN* 3.3 5.4 + - - -
101C HIS* 3.1 31.1 + - - +
103C ILE* 4.5 9.4 - - - +
123C ARG* 2.7 53.4 + - - -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B ASN 5.4 2.9 + - - -
48B GLU* 3.0 29.4 - - - +
94B ASN 4.3 1.1 - - - +
95B GLU* 1.3 78.2 - - - +
97B GLN* 1.3 74.1 + - + +
127B VAL* 2.7 15.3 + - + +
128B LEU 4.2 2.7 - - - -
129B SER* 3.6 40.3 - - - +
38C THR* 3.6 23.0 + - + +
40C SER* 3.6 28.2 + - - -
41C LYS* 6.3 1.1 - - - +
52C GLN* 3.8 14.6 - - - +
99C TYR* 6.1 0.3 - - - -
101C HIS* 3.4 13.9 + - - -
125C SER* 3.9 7.8 + - - -
177C SER* 4.7 3.8 + - - -
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B GLU* 5.1 3.6 + - - -
95B GLU* 3.3 10.0 + - - +
96B LYS* 1.3 89.2 - - + +
98B ALA* 1.3 64.0 + - - +
99B TYR* 3.4 25.2 + - + +
126B LEU* 3.5 0.4 - - - -
127B VAL* 2.8 59.2 + - + +
41C LYS* 4.8 13.9 - - - +
99C TYR* 6.5 1.1 - - + -
101C HIS* 5.0 1.1 - - - -
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B GLU* 3.5 17.2 + - + +
97B GLN* 1.3 78.1 - - - +
99B TYR* 1.3 75.2 + - - +
125B SER 3.2 5.8 - - - -
126B LEU* 3.3 24.7 - - + -
101C HIS* 5.7 0.2 - - - -
103C ILE* 3.9 24.2 + - + +
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Residues in contact with TYR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLN* 3.4 33.6 + - + +
98B ALA* 1.3 88.4 - - - +
100B LYS* 1.3 67.6 + - - +
101B HIS* 5.1 4.0 - - + -
124B ILE* 3.5 5.0 - - - +
125B SER* 2.9 52.7 + - - +
127B VAL* 5.1 7.2 - - + -
103C ILE* 4.5 2.9 - - - -
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B TYR* 1.3 79.5 - - - +
101B HIS* 1.3 68.1 + - - +
102B THR* 3.7 17.9 + - + +
108B VAL* 5.2 2.0 - - - +
120B TYR* 3.2 25.7 + - - -
122B VAL* 3.4 20.0 - - + +
123B ARG 3.9 11.9 - - - +
124B ILE* 4.6 3.0 - - + +
102C THR 4.9 1.8 - - - +
103C ILE* 4.0 14.8 - - + +
104C ASP* 3.3 39.3 + - - +
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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