Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 6ABP
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 PRO 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85A VAL 3.8 16.2 - - - +
86A ILE* 4.2 12.8 - - + -
87A ALA* 2.9 26.2 + - - +
102A THR 3.5 8.3 - - - +
103A VAL* 1.3 86.1 - - - +
105A LEU* 1.4 58.4 + - - +
106A VAL* 6.4 0.2 - - + -
266A MET* 6.2 1.1 - - + -
270A TRP* 4.0 18.2 - - + -
276A GLU* 5.6 1.1 - - - +
277A PRO* 3.8 34.3 - - + +
278A PRO 3.6 16.4 - - - +
279A LYS* 3.4 17.2 - - + +
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.3 25.6 - - + +
89A ASP 4.3 7.6 - - - +
90A ASP 4.2 2.9 - - - -
91A GLN* 3.6 54.7 - - + +
103A VAL 4.2 4.7 - - - +
104A PRO* 1.4 76.3 - - - +
106A VAL* 1.3 82.7 - - - +
107A MET* 3.9 10.5 - - + -
278A PRO 5.1 0.7 - - - +
279A LYS 2.9 11.9 + - - +
280A PHE* 3.6 26.7 - - + -
281A THR* 2.9 25.3 + - - -
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ILE* 4.5 5.6 - - + -
87A ALA 3.0 9.6 + - - +
88A VAL* 3.4 9.7 - - + +
89A ASP 2.9 24.3 + - - -
104A PRO* 6.4 0.2 - - + -
105A LEU* 1.3 78.6 - - - +
107A MET* 1.3 63.1 + - - +
258A VAL 5.2 1.1 - - - +
259A HIS* 4.3 31.6 - - + +
262A LYS* 5.3 3.8 - - + -
263A SER* 4.1 13.9 - - - +
266A MET* 3.3 34.8 - - + -
281A THR* 3.4 18.6 - - + +
283A VAL* 4.4 12.1 - - + -
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Residues in contact with MET 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ASP* 3.8 23.1 - - - +
91A GLN* 5.4 4.7 - - - +
105A LEU* 3.9 15.9 - - + -
106A VAL* 1.3 77.7 - - - +
108A LEU* 1.3 79.2 + - + +
110A ALA* 4.3 4.0 - - + -
146A ASP* 5.7 0.4 - - - +
147A THR* 3.3 30.7 - - - +
150A ARG* 3.9 24.0 - - - +
259A HIS* 3.6 14.1 - - - -
280A PHE* 3.8 31.4 - - + -
281A THR 2.9 8.7 + - - -
282A GLU* 3.3 5.4 - - - +
283A VAL* 2.8 24.4 + - - +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A TRP* 4.2 14.6 - - + -
89A ASP* 4.9 0.4 + - - +
107A MET* 1.3 96.4 - - + +
109A ALA* 1.3 62.8 + - - +
110A ALA* 3.0 33.5 + - + +
113A ILE* 4.1 12.6 - - + -
147A THR* 4.6 4.0 - - - +
150A ARG* 5.5 0.2 + - - -
151A ARG* 4.3 31.9 - - - +
231A ILE* 4.5 7.2 - - + -
254A PRO* 4.0 30.5 - - + -
259A HIS* 3.4 16.4 - - + +
282A GLU* 3.9 2.6 - - - +
283A VAL 3.4 10.8 - - - +
307A ARA 4.7 6.1 - - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 1.3 70.3 - - - +
110A ALA* 1.3 56.4 + - - +
111A THR 3.5 2.5 - - - -
112A LYS* 4.0 18.4 - - + -
113A ILE* 2.9 36.7 + - + +
150A ARG* 4.8 0.2 - - - -
282A GLU* 3.4 34.0 - - + +
283A VAL 3.1 13.6 + - - +
284A THR* 4.0 17.0 - - + -
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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