Contacts of the strand formed by residues 54 - 62 (chain M) in PDB entry 6E0P
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 TYR 54 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C GLU* 5.0 3.4 + - - -
104D GLY* 5.3 2.6 - - - -
105D GLU* 3.2 45.1 + - + +
49M TYR* 3.4 35.1 - + + +
50M THR* 3.6 8.7 - - - -
51M PHE 3.7 7.0 + - - +
52M THR 3.2 1.0 + - - -
53M SER* 1.3 94.7 - - - +
55M THR* 1.3 64.1 + - - +
56M ILE* 4.7 2.8 - - - +
74M TYR* 4.0 5.6 - - - -
75M PRO* 3.3 18.7 - - - +
120M ARG* 3.5 49.7 + - + -
121M LYS 3.6 2.0 - - - +
122M SER* 3.6 23.1 - - - +
123M SER 4.9 0.2 - - - +
130M ASP* 5.0 1.3 - - - -
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Residues in contact with THR 55 (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* 1.3 77.4 - - - +
56M ILE* 1.3 63.1 + - - +
57M GLN* 3.2 25.5 + - - +
72M TYR* 3.9 22.2 - - + -
73M ILE 3.4 10.8 - - - -
74M TYR* 3.5 24.6 - - + -
120M ARG* 3.9 1.4 - - - -
121M LYS* 2.7 50.7 + - - +
122M SER* 4.6 1.1 - - - +
123M SER* 4.8 13.7 - - - -
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Residues in contact with ILE 56 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26M LEU* 4.9 4.7 - - + -
44M CYS* 4.0 32.1 - - - +
46M ALA* 4.6 1.3 - - + -
49M TYR* 3.9 17.0 - - - +
51M PHE* 3.6 31.2 - - + -
54M TYR 3.9 4.0 + - - +
55M THR* 1.3 77.0 - - - +
57M GLN* 1.3 65.5 + - - +
58M TRP* 3.6 22.3 + - - +
72M TYR* 3.3 3.3 - - - -
73M ILE* 3.1 30.6 + - - +
75M PRO* 4.7 2.4 - - + +
101M VAL* 3.7 24.5 - - + -
118M CYS* 4.1 1.3 - - + -
119M ALA 3.3 9.9 - - - +
120M ARG* 5.1 0.9 - - - -
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Residues in contact with GLN 57 (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 THR* 3.2 19.7 + - - +
56M ILE* 1.3 73.9 - - - +
58M TRP* 1.3 62.6 + - - +
59M VAL* 5.4 0.2 - - + -
69M TRP* 2.5 39.1 + - + +
71M GLY 3.4 6.1 - - - -
72M TYR* 3.3 26.9 - - - +
118M CYS* 3.3 5.4 - - - +
119M ALA* 2.7 34.9 + - + +
121M LYS* 3.5 31.0 - - + +
129M LEU* 3.6 29.0 - - + +
254M TYR* 3.5 11.1 + - - -
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Residues in contact with TRP 58 (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* 3.8 15.3 - - - -
42M MET* 4.1 25.1 - - + -
43M PRO 4.4 2.7 - - - -
44M CYS* 3.7 18.4 - - + -
56M ILE* 3.6 13.6 + - - +
57M GLN* 1.3 77.9 - - - +
59M VAL* 1.3 60.6 - - - +
69M TRP* 3.8 2.9 - - - -
70M ILE* 2.8 46.9 + - + +
71M GLY 2.8 13.6 + - - +
92M LEU* 3.5 35.2 - - + +
101M VAL* 3.6 38.7 - - + +
103M MET* 3.6 31.2 - - + -
116M TYR* 4.9 4.0 - - + -
117M TYR 3.4 17.3 - - - -
118M CYS* 3.7 21.1 - - + -
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Residues in contact with VAL 59 (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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57M GLN 5.1 0.4 - - - -
58M TRP* 1.3 82.3 - - - +
60M LYS* 1.3 63.9 - - - +
67M LEU* 3.7 29.2 - - + -
68M GLU 3.4 12.3 - - - +
69M TRP* 4.7 5.4 - - + -
70M ILE* 3.9 3.8 - - - +
115M VAL 3.7 0.5 - - - +
116M TYR* 3.5 4.0 - - - +
117M TYR* 2.9 38.6 + - + +
119M ALA* 5.0 3.8 - - + -
129M LEU* 4.0 11.0 - - + -
132M TRP* 4.0 23.3 - - + -
256M PHE* 3.8 32.3 - - + -
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Residues in contact with LYS 60 (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 VAL* 1.3 74.2 - - - +
61M GLN* 1.3 62.3 + - - +
62M THR* 3.7 25.2 - - + +
65M GLN* 5.9 0.6 + - - -
66M GLY 3.6 1.4 - - - +
67M LEU* 3.4 2.9 - - - -
68M GLU* 2.7 50.7 + - + +
70M ILE* 3.7 18.2 - - + +
86M PHE* 3.6 29.5 - - + -
111M GLU 3.0 26.2 + - - -
112M ASP* 3.5 11.5 + - - +
114M ALA* 3.7 10.3 - - + -
115M VAL 3.7 3.1 - - - -
116M TYR* 3.5 29.8 + - + +
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Residues in contact with GLN 61 (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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60M LYS* 1.3 73.9 - - - +
62M THR* 1.3 65.5 + - - +
63M PRO* 4.2 4.4 - - + +
66M GLY* 3.4 9.6 - - - +
67M LEU* 3.7 20.8 - - + +
114M ALA* 3.3 6.2 - - - +
115M VAL* 2.9 42.9 + - + +
117M TYR* 3.2 18.8 + - + -
196M GLN* 2.9 42.3 + - - +
245M TYR* 3.9 13.7 + - - -
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Residues in contact with THR 62 (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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60M LYS* 3.7 32.4 - - + +
61M GLN* 1.3 76.9 - - - +
63M PRO* 1.3 64.7 - - - +
64M ARG* 3.0 11.2 + - + -
65M GLN* 3.1 35.3 + - - +
66M GLY* 3.0 26.9 + - - +
68M GLU* 5.7 2.0 - - - +
111M GLU 5.7 2.5 - - - +
113M SER 4.3 7.4 - - - +
114M ALA* 3.7 10.3 - - + -
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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