Contacts of the strand formed by residues 104 - 109 (chain B) in PDB entry 4TR8
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 SER 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A ARG* 3.6 8.7 + - - -
304A GLU 3.4 7.4 - - - -
305A GLU* 3.1 27.4 + - - -
82B LEU* 4.1 7.5 - - - +
83B PRO* 5.6 0.9 - - - +
100B LYS* 3.5 4.7 - - - +
101B ALA 2.9 35.8 + - - -
102B GLY 3.4 1.8 - - - +
103B ARG* 1.4 78.7 + - - +
105B ARG* 1.3 64.8 + - - +
106B PHE* 3.7 24.0 - - - -
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Residues in contact with ARG 105 (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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302A GLU 4.6 0.4 - - - -
303A ALA* 3.3 3.6 - - - -
304A GLU* 2.8 58.5 + - + +
98B LEU* 5.1 12.9 - - - +
99B VAL 3.3 5.4 - - - +
100B LYS* 3.7 34.5 - - + +
103B ARG 5.3 2.7 - - - +
104B SER* 1.3 80.7 - - - +
106B PHE* 1.3 67.8 + - - +
107B THR* 6.1 0.2 - - - +
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Residues in contact with PHE 106 (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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270A ARG* 3.8 43.5 - - + -
271A THR* 4.8 1.8 - - + -
273A ILE* 5.3 0.2 - - + -
274A LEU* 4.0 7.0 - - + -
302A GLU 3.3 4.9 - - - -
303A ALA* 3.7 22.4 - - + -
304A GLU 5.5 0.9 - - - -
305A GLU* 5.5 0.7 - - - -
78B ILE* 3.7 51.8 - - + -
81B SER* 5.1 0.2 - - - -
82B LEU* 4.0 8.5 - - + -
97B LEU 3.6 0.7 - - - +
98B LEU* 3.4 4.3 - - - +
99B VAL* 2.8 55.0 + - + -
100B LYS* 5.8 0.2 - - - -
101B ALA* 5.9 0.7 - - + -
104B SER* 3.7 28.9 - - - -
105B ARG* 1.3 76.7 - - - +
107B THR* 1.3 65.1 + - - +
108B LEU* 4.1 1.8 - - + -
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Residues in contact with THR 107 (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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274A LEU* 3.8 2.8 - - - +
300A GLN 5.1 5.8 - - - +
301A GLU* 3.3 11.1 - - - +
302A GLU* 2.8 44.7 + - - +
96B LYS* 3.8 35.4 - - + +
97B LEU 3.3 2.9 - - - -
98B LEU* 4.1 16.1 - - + +
106B PHE* 1.3 73.8 + - - +
108B LEU* 1.3 60.6 + - - +
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Residues in contact with LEU 108 (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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274A LEU* 3.8 32.8 - - + -
301A GLU* 3.9 9.6 - - - +
70B VAL* 4.7 6.7 - - + -
71B PRO* 4.7 6.5 - - + +
74B LYS* 4.3 8.7 - - + -
75B LEU* 3.9 39.5 - - + +
78B ILE* 3.8 22.0 - - + -
96B LYS* 3.4 10.4 - - - +
97B LEU* 2.8 53.2 + - + +
99B VAL* 4.9 2.9 - - + -
106B PHE* 5.1 2.9 - - + -
107B THR* 1.3 74.5 - - - +
109B SER* 1.3 69.0 + - - +
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Residues in contact with SER 109 (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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299A GLU* 4.6 15.4 - - - +
301A GLU* 3.0 30.2 + - - +
32B ASN* 5.7 0.2 - - - -
70B VAL* 4.2 0.2 - - - -
71B PRO* 3.2 28.9 - - - +
96B LYS* 4.2 15.0 - - - +
108B LEU* 1.3 75.6 - - - +
110B THR* 1.3 64.7 + - - +
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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