Contacts of the strand formed by residues 96 - 102 (chain B) in PDB entry 4P5K
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 96 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A GLU* 4.4 11.7 - - - +
94B GLN* 4.2 11.7 + - - +
95B PRO* 1.3 77.0 + - - +
97B VAL* 1.3 61.1 + - - +
116B HIS 3.8 0.2 - - - +
117B VAL* 3.2 4.7 - - - +
118B THR* 2.6 52.3 + - - +
119B ASP* 4.1 19.7 - - + -
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Residues in contact with VAL 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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95B PRO* 4.9 3.4 - - + +
96B ARG* 1.3 83.1 - - - +
98B ASN* 1.3 61.5 + - - +
115B CYS* 5.3 2.5 - - - -
116B HIS 3.5 2.2 - - - +
117B VAL* 4.0 15.0 - - + -
173B VAL* 3.8 37.0 - - + -
182B VAL* 3.9 19.7 - - + -
184B VAL* 3.8 32.6 - - + +
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Residues in contact with ASN 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PRO* 3.8 37.5 - - + +
97B VAL* 1.3 77.0 - - - +
99B VAL* 1.3 69.8 + - - +
100B SER* 3.6 20.5 + - - -
114B VAL 3.3 1.7 - - - +
115B CYS* 3.7 2.3 - - - -
116B HIS* 2.8 40.1 + - + +
184B VAL* 5.5 0.7 - - - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 1.3 83.9 + - - +
100B SER* 1.3 68.0 + - - +
101B PRO* 4.8 1.0 - - - +
113B LEU* 4.3 24.0 - - + -
114B VAL 3.4 6.5 - - - +
115B CYS* 4.1 17.0 - - + -
129B TRP* 4.4 7.4 - - + -
171B CYS* 4.4 3.6 - - + -
184B VAL* 3.8 43.5 - - + +
185B GLU 5.1 3.4 - - - +
186B TRP* 4.5 21.8 - - + +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASN* 3.6 17.6 + - - -
99B VAL* 1.3 78.1 + - - +
101B PRO* 1.3 78.2 - - - +
113B LEU* 3.6 7.2 - - - +
114B VAL* 2.9 38.7 + - - +
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Residues in contact with PRO 101 (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 VAL 4.8 0.2 - - - +
100B SER* 1.3 97.4 - - - +
102B SER* 1.3 71.5 + - - +
103B LYS* 3.9 25.1 - - + +
112B LEU 3.6 7.2 - - - +
113B LEU* 4.2 7.2 - - + -
114B VAL* 4.4 1.2 - - - +
161B MET* 5.7 0.9 - - + -
186B TRP* 3.6 34.1 - - + -
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Residues in contact with SER 102 (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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101B PRO* 1.3 79.2 + - - +
103B LYS* 1.3 64.0 + - - +
104B LYS 3.4 11.5 + - - +
110B HIS* 4.5 10.6 + - - -
111B ASN* 5.1 0.2 + - - -
112B LEU* 3.0 39.0 + - - +
114B VAL* 3.8 14.1 - - - +
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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
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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