Contacts of the strand formed by residues 111 - 117 (chain M) in PDB entry 6D6Q
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 THR 111 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103M SER* 5.0 2.4 + - - -
106M THR* 4.9 2.9 - - - -
110M CYS* 1.3 77.4 - - - +
112M HIS* 1.3 62.9 + - - +
113M GLU* 4.0 20.8 + - + +
306M VAL* 3.6 2.1 - - + +
307M ILE* 3.4 5.5 - - - +
308M TYR* 2.8 58.1 + - + +
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Residues in contact with HIS 112 (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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103M SER* 3.7 2.3 + - - -
104M VAL* 3.1 47.7 + - + +
106M THR* 4.4 9.9 + - + +
111M THR* 1.3 74.6 + - - +
113M GLU* 1.3 82.5 + - - +
114M VAL* 4.5 0.6 - - + +
122M TYR* 5.6 1.1 - - - -
125M LEU* 4.6 14.4 - - + -
146M GLU* 3.8 26.5 + - + +
150M CYS* 5.4 1.7 - - + +
305M HIS* 3.1 39.6 + + - +
306M VAL 3.2 9.2 - - - -
307M ILE* 3.2 28.5 - - + +
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Residues in contact with GLU 113 (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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101M VAL* 5.2 2.5 - - + -
102M GLN 3.3 9.0 - - - +
103M SER* 3.8 24.4 + - - +
104M VAL* 4.8 0.7 - - - +
111M THR* 4.0 17.7 + - + +
112M HIS* 1.3 85.4 - - - +
114M VAL* 1.3 64.5 + - - +
290M ARG* 2.6 45.1 + - + +
306M VAL* 2.8 48.7 + - + +
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Residues in contact with VAL 114 (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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100M LYS 4.9 0.2 - - - -
101M VAL* 3.2 8.0 - - - +
102M GLN* 2.9 57.2 + - + +
104M VAL* 4.7 5.8 - - + -
112M HIS* 4.5 3.1 - - - +
113M GLU* 1.3 75.5 - - - +
115M ALA* 1.3 62.1 + - - +
116M LEU* 4.2 8.7 - - + -
122M TYR* 3.8 35.4 - - + +
293M ALA* 5.6 0.7 - - - -
303M PRO* 6.3 1.6 - - + -
304M CYS 3.3 6.1 - - - +
305M HIS* 3.0 41.3 - - + +
306M VAL* 5.6 0.2 - - - -
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Residues in contact with ALA 115 (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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99M VAL* 4.9 0.4 - - + -
100M LYS 3.7 5.6 - - - +
101M VAL* 4.4 4.9 - - + +
113M GLU 4.3 0.2 + - - -
114M VAL* 1.3 73.9 - - - +
116M LEU* 1.3 62.4 + - - +
293M ALA* 3.5 43.3 - - + +
294M GLU* 3.8 16.6 - - + +
297M CYS* 4.0 6.4 - - + +
303M PRO* 3.4 2.3 - - - +
304M CYS 2.9 32.6 + - - +
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Residues in contact with LEU 116 (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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99M VAL* 3.6 5.0 - - - +
100M LYS* 2.9 56.8 + - + +
102M GLN* 5.1 2.5 - - + -
114M VAL* 4.2 14.8 - - + -
115M ALA* 1.3 74.3 - - - +
117M PRO* 1.3 105.3 - - + +
120M GLU* 3.0 24.7 - - + +
121M ASP 4.8 1.1 - - - +
122M TYR* 4.0 35.4 - - + -
297M CYS* 3.2 8.0 - - - -
303M PRO* 4.2 12.8 - - + -
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Residues in contact with PRO 117 (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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98M ARG 5.3 1.6 - - - +
99M VAL* 5.1 1.3 - - - -
116M LEU* 1.3 107.1 - - + +
118M ALA* 1.3 55.8 + - - +
119M GLU* 2.8 16.0 + - + +
120M GLU* 3.2 43.6 + - + +
297M CYS* 3.3 15.7 - - - -
301M LYS* 3.8 25.4 - - + +
303M PRO* 4.5 9.2 - - + -
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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