Contacts of the strand formed by residues 103 - 109 (chain M) in PDB entry 7K63
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 ALA 103 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56M GLN* 3.5 26.7 - - + -
57M GLN 3.3 23.6 - - - +
58M LYS* 3.6 10.3 - - + +
59M PRO* 4.9 4.5 - - - -
101M ASP 3.2 4.2 + - - +
102M THR* 1.3 75.7 + - - +
104M THR* 1.3 62.9 + - - +
105M TYR* 3.6 7.1 - - + -
122M LYS* 4.7 5.8 - - - +
123M LEU* 2.9 30.4 + - - +
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Residues in contact with THR 104 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M TYR 3.8 0.3 - - - +
56M GLN* 3.6 1.0 - - - -
57M GLN* 2.7 46.8 + - - +
59M PRO* 5.9 1.2 - - - +
103M ALA* 1.3 72.8 - - - +
105M TYR* 1.3 62.2 + - - +
106M TYR* 3.5 36.0 + - + +
120M GLY* 3.8 16.6 - - - +
121M THR 3.4 13.5 - - - +
122M LYS* 3.9 18.2 - - + +
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Residues in contact with TYR 105 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25M GLN* 2.9 24.8 + - - +
40M ILE* 3.9 26.0 - - + -
54M TRP* 4.7 2.0 - - + -
55M TYR 3.1 15.9 - - - +
56M GLN* 3.1 25.4 + - + -
66M LEU* 3.6 22.4 - - + -
81M PHE* 3.8 8.3 - + - -
92M LEU* 3.7 18.6 - - + -
94M ILE* 3.7 16.8 - - + +
101M ASP* 2.6 25.4 + - - -
103M ALA 3.6 20.0 - - - -
104M THR* 1.3 72.4 - - - +
106M TYR* 1.3 61.2 + - - +
120M GLY* 3.3 0.9 - - - -
121M THR 3.0 24.9 + - - +
123M LEU* 3.7 22.0 - - + -
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Residues in contact with TYR 106 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25M GLN* 3.6 2.2 - - - -
54M TRP* 3.4 5.0 - - - -
55M TYR* 2.8 46.3 + - + -
57M GLN* 3.1 33.3 + - + -
63M PRO* 5.5 0.2 - - + -
104M THR* 3.5 36.3 + - + +
105M TYR* 1.3 73.4 - - - +
107M CYS* 1.3 68.2 + - - +
117M PHE* 4.2 6.3 - - + -
118M GLY 3.6 13.7 - - - -
119M SER 3.7 9.1 + - - -
120M GLY* 3.5 22.2 - - - -
188M GLN* 3.7 9.4 + - - -
193M GLY* 5.2 4.9 - - - -
194M LEU* 3.5 37.9 - - + -
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Residues in contact with CYS 107 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23M MET* 3.5 12.8 - - + -
25M GLN* 3.5 15.6 + - - -
42M CYS* 3.4 30.7 - - - -
52M LEU* 4.1 6.3 - - + -
53M SER 3.2 8.3 - - - +
54M TRP* 3.9 20.6 - - + -
106M TYR* 1.3 73.7 - - - +
108M LEU* 1.3 62.7 + - - +
109M GLN 4.3 0.2 - - - -
117M PHE* 3.2 7.3 - - - -
118M GLY* 2.9 44.3 + - - -
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Residues in contact with LEU 108 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23M MET* 4.2 2.0 - - - -
51M TYR 3.7 0.9 - - - +
52M LEU* 3.4 3.6 - - - +
53M SER* 2.7 29.6 + - - +
55M TYR* 3.3 41.3 - - + +
107M CYS* 1.3 76.8 - - - +
109M GLN* 1.3 78.3 + - - +
110M HIS* 3.8 11.2 + - + +
115M TYR* 3.8 18.6 - - + -
116M THR 3.5 10.5 - - - +
117M PHE* 3.6 33.0 - - + -
196M TRP* 6.2 0.2 - - + -
255M THR* 4.2 6.1 - - - +
256M LEU* 3.9 17.7 - - + -
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Residues in contact with GLN 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M ILE* 3.9 29.0 - - + +
23M MET* 3.5 36.7 - - + +
48M ILE* 3.7 19.5 - - + +
51M TYR 3.4 5.4 - - - -
108M LEU* 1.3 76.0 - - - +
110M HIS* 1.3 62.2 + - - +
111M GLY 3.1 16.1 + - - -
112M GLU 3.6 8.4 + - - -
114M PRO 2.6 30.5 + - - -
115M TYR* 3.4 4.9 - - - -
116M THR* 3.1 40.8 + - - +
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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