Contacts of the strand formed by residues 126 - 134 (chain M) in PDB entry 1YHQ
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 GLN 126 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32M ARG* 3.8 15.3 - - - +
66M SER* 3.6 22.5 + - - -
67M VAL 3.3 17.9 - - - +
68M ARG* 4.3 1.1 - - - -
69M LYS* 3.3 10.6 - - - +
122M GLN* 3.1 20.8 - - - +
123M ASP* 2.9 39.6 + - - +
125M ARG* 1.3 96.7 - - + +
127M LYS* 1.3 63.2 + - - +
128M TRP* 3.4 28.9 - - + -
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Residues in contact with LYS 127 (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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4020 U 4.9 6.3 + - - -
4030 C 2.7 40.8 + - - -
4040 G 5.4 1.1 + - - -
65M VAL 3.5 0.7 - - - +
66M SER* 3.2 4.9 - - - -
67M VAL* 2.8 36.2 + - - +
69M LYS* 3.6 9.0 - - + +
97M ILE* 4.0 28.1 - - + +
121M GLY 3.7 5.6 - - - +
122M GLN* 3.2 33.1 + - + +
126M GLN* 1.3 77.6 - - - +
128M TRP* 1.3 64.4 + - - +
129M HIS* 4.2 20.4 + - + -
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Residues in contact with TRP 128 (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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28M GLN* 3.6 33.7 - - + -
31M TRP* 3.5 44.3 + + + +
32M ARG* 4.0 12.8 - - + -
64M ARG* 3.8 22.9 - - + -
65M VAL 3.2 3.4 - - - +
66M SER* 3.2 30.3 - - - -
119M SER* 3.8 2.6 + - - -
120M VAL* 3.0 39.4 + - + -
121M GLY 3.0 13.2 + - - +
122M GLN* 3.9 11.4 - - - -
123M ASP* 3.4 35.0 - - - -
126M GLN* 3.4 24.5 - - + -
127M LYS* 1.3 75.4 - - - +
129M HIS* 1.3 68.2 + - - +
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Residues in contact with HIS 129 (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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63M ALA 3.7 0.3 - - - +
64M ARG* 3.3 1.7 - - - -
65M VAL* 2.8 32.5 + - - +
67M VAL* 5.7 0.2 - - - +
97M ILE* 4.2 13.8 - - + +
98M GLN* 3.5 50.3 + - + +
101M ALA* 4.2 20.4 - - + +
117M SER* 5.1 3.1 - - - +
118M TYR 3.2 10.1 - - - +
119M SER* 3.5 33.4 - - - -
120M VAL* 4.2 1.6 - - - -
127M LYS* 4.2 19.0 + - + +
128M TRP* 1.3 79.8 + - - +
130M GLU* 1.3 67.1 + - - +
131M VAL* 4.0 4.0 + - + -
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Residues in contact with GLU 130 (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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40M ILE* 3.1 21.6 - - - +
43M PRO* 3.8 0.7 - - - +
44M THR* 2.7 38.8 + - - -
62M VAL* 4.3 8.2 - - + +
63M ALA 3.3 6.5 - - - +
64M ARG* 3.4 20.2 + - + -
117M SER* 3.3 2.9 - - - -
118M TYR* 2.6 73.0 + - + +
120M VAL* 3.4 24.6 - - + +
129M HIS* 1.3 76.4 - - - +
131M VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 131 (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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62M VAL* 3.3 6.4 - - - -
63M ALA 2.8 37.9 + - - +
65M VAL* 4.4 6.3 - - + -
101M ALA* 4.3 6.5 - - + +
102M GLU* 4.1 14.6 - - + +
105M ALA* 4.0 23.8 - - + -
114M VAL* 3.7 24.7 - - + -
116M ASN 3.7 11.2 - - - +
117M SER* 3.9 12.6 - - - -
129M HIS* 4.6 4.3 - - + +
130M GLU* 1.3 77.0 - - - +
132M ILE* 1.3 64.4 + - - +
133M LEU* 3.4 22.3 - - + +
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Residues in contact with ILE 132 (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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49M ALA* 3.9 36.3 - - + +
52M GLN* 4.0 21.8 - - + +
54M TYR* 4.0 14.8 - - + +
60M VAL* 4.4 10.8 - - + -
61M ILE 3.3 9.4 - - - +
62M VAL* 4.6 11.0 - - + -
114M VAL* 3.7 2.4 - - - -
115M LEU* 2.8 44.0 + - + +
116M ASN* 2.9 16.2 + - + +
118M TYR* 4.4 10.3 - - + -
131M VAL* 1.3 76.5 - - - +
133M LEU* 1.3 62.5 + - - +
134M ILE* 4.3 13.2 - - + -
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Residues in contact with LEU 133 (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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59M GLY 3.8 0.3 - - - +
61M ILE* 2.7 46.9 + - + +
63M ALA* 4.6 14.1 - - + -
105M ALA* 4.1 5.4 - - + +
106M SER* 4.1 21.8 - - - +
109M PHE* 3.7 26.9 - - + -
112M LEU* 3.8 27.1 - - + -
113M ARG 3.3 10.1 - - - +
114M VAL* 4.5 7.6 - - + -
131M VAL* 3.4 35.0 - - + +
132M ILE* 1.3 76.2 - - - +
134M ILE* 1.3 67.3 + - - +
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Residues in contact with ILE 134 (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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53M GLY 5.7 1.8 - - - +
54M TYR* 6.1 0.2 - - - -
59M GLY 3.3 1.3 - - - -
60M VAL* 3.8 29.4 - - + -
112M LEU* 3.6 5.2 - - - -
113M ARG* 2.9 24.1 + - - +
115M LEU* 3.8 27.8 - - + -
132M ILE* 4.3 9.9 - - + -
133M LEU* 1.3 86.3 - - - +
135M ASP* 1.3 63.0 + - - +
136M PRO* 2.9 15.1 - - - +
141M ILE* 3.3 35.4 - - + -
147M LEU* 4.6 13.7 - - + -
150M ILE* 3.8 24.4 - - + +
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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