Contacts of the strand formed by residues 114 - 122 (chain M) in PDB entry 6E0C
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 114 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M LYS* 3.7 25.1 - - + -
61M GLN 3.4 15.9 - - - +
62M THR* 3.7 16.4 - - + +
63M PRO* 5.8 1.1 - - - -
112M ASP 3.1 4.9 + - - -
113M SER* 1.3 76.3 - - - +
115M VAL* 1.3 62.2 + - - +
116M TYR* 4.0 10.1 - - + -
136M THR 3.6 0.5 - - - +
137M SER* 3.6 3.0 + - - -
138M VAL* 2.8 32.5 + - - +
139M THR* 5.9 0.2 - - - +
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Residues in contact with VAL 115 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M VAL 3.9 0.7 - - - +
60M LYS* 3.6 2.3 - - - -
61M GLN* 2.9 40.4 + - - +
114M ALA* 1.3 77.6 - - - +
116M TYR* 1.3 63.8 + - - +
117M TYR* 3.7 35.5 + - + +
134M GLN 4.7 1.6 - - - +
135M GLY* 3.8 20.4 - - - -
136M THR 3.4 8.3 - - - +
137M SER* 4.3 16.6 - - - +
199M TRP* 5.0 17.0 - - + -
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Residues in contact with TYR 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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28M GLN* 2.6 30.5 + - - -
42M MET* 3.7 22.4 - - + -
58M TRP* 4.7 4.0 - - + -
59M VAL 3.5 2.2 - - - -
60M LYS* 3.4 42.7 + - + -
70M ILE* 3.6 26.0 - - + -
86M PHE* 5.2 3.0 - + - -
103M MET* 4.3 10.5 - - + -
105M LEU* 3.7 31.3 - - + +
112M ASP* 3.5 29.5 + - - +
114M ALA* 4.0 14.4 - - + -
115M VAL* 1.3 74.6 - - - +
117M TYR* 1.3 56.6 + - - +
135M GLY* 4.3 0.2 - - - -
136M THR* 3.1 21.7 + - - +
138M VAL* 4.2 14.8 - - + -
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Residues in contact with TYR 117 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M GLN* 3.9 3.6 - - - +
58M TRP* 3.5 8.1 - - - -
59M VAL* 2.9 38.4 + - + +
61M GLN* 3.0 41.7 + - + -
67M LEU* 4.8 4.5 - - + -
115M VAL* 3.7 22.2 - - + +
116M TYR* 1.3 74.1 - - - +
118M CYS* 1.3 60.0 + - - +
132M TRP* 3.6 30.7 - + + -
133M GLY 3.2 20.2 - - - +
134M GLN 3.5 19.4 + - - -
135M GLY* 3.9 6.7 - - - -
196M GLN* 3.1 16.5 + - - -
199M TRP* 5.4 1.2 - - - -
200M LYS 3.2 7.5 + - - -
201M SER* 3.7 15.5 - - - -
202M PRO* 4.0 9.0 - - + -
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Residues in contact with CYS 118 (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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26M LEU* 3.5 7.2 - - - +
28M GLN* 3.6 25.3 + - - +
44M CYS* 2.0 49.1 - - + -
56M ILE* 4.1 2.5 - - + -
57M GLN 3.2 8.1 - - - +
58M TRP* 3.7 22.2 - - + -
117M TYR* 1.3 74.6 - - - +
119M ALA* 1.3 59.2 + - - +
132M TRP* 3.5 0.7 - - - -
133M GLY* 2.8 30.4 + - - -
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Residues in contact with ALA 119 (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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26M LEU* 4.0 4.3 - - - -
56M ILE* 3.3 2.8 - - - -
57M GLN* 2.5 44.2 + - + +
59M VAL* 5.0 1.3 - - + -
117M TYR 4.1 0.4 - - - -
118M CYS* 1.3 75.4 - - - +
120M ARG* 1.3 60.3 + - - +
129M LEU* 3.7 37.5 - - + -
131M TYR 3.3 9.4 - - - +
132M TRP* 3.9 18.4 - - + -
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Residues in contact with ARG 120 (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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105D GLU* 5.1 4.9 + - - -
24M VAL* 3.5 18.7 - - - +
26M LEU* 3.8 15.8 - - + +
49M TYR* 3.4 56.1 - - - +
54M TYR* 3.5 47.4 + - + -
55M THR 3.6 5.2 - - - +
56M ILE* 4.6 1.6 - - + +
119M ALA* 1.3 72.3 - - - +
121M LYS* 1.3 59.5 + - - +
129M LEU* 3.4 1.4 - - - -
130M ASP* 2.8 52.1 + - - +
131M TYR* 2.9 47.1 + - + +
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Residues in contact with LYS 121 (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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54M TYR* 3.5 5.6 - - - -
55M THR* 2.7 49.2 + - + +
57M GLN* 3.5 28.9 - - + +
119M ALA 3.9 0.8 + - - -
120M ARG* 1.3 74.1 - - - +
122M SER* 1.3 73.3 + - - +
123M SER* 4.9 1.2 - - - +
124M ARG 3.3 18.2 + - - -
125M LEU* 4.6 4.8 + - - +
127M SER 3.3 16.6 + - - +
128M THR* 3.5 20.6 - - - +
129M LEU* 3.9 15.5 - - + -
130M ASP* 4.3 0.9 - - - -
249M HIS* 4.4 13.2 - - - -
254M TYR* 4.1 21.9 + - + +
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Residues in contact with SER 122 (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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92C GLU* 4.3 4.7 + - - -
105D GLU* 3.4 24.0 - - - +
53M SER 4.5 1.7 + - - -
54M TYR* 3.6 23.4 - - - -
55M THR* 4.5 3.2 - - - +
121M LYS* 1.3 104.7 + - - +
123M SER* 1.3 67.8 + - - +
124M ARG* 3.1 13.1 + - - +
127M SER* 3.6 26.6 - - - -
130M ASP* 4.3 3.6 + - - -
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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