Contacts of the strand formed by residues 64 - 73 (chain M) in PDB entry 5X22
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 LEU 64 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55M GLU 3.9 0.5 - - - -
56M GLU* 3.4 26.4 + - - -
63M GLY* 1.3 73.2 - - - -
65M VAL* 1.3 62.5 + - - +
100M LEU* 3.7 28.5 - - + -
101M ILE 3.7 1.1 - - - -
102M HIS* 3.5 37.0 - - + +
359M MET* 3.7 33.9 - - + +
364M GLU* 4.2 25.6 - - - +
365M ASP 6.1 0.4 - - - +
367M LEU* 3.6 33.9 - - + -
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Residues in contact with VAL 65 (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 PRO* 4.4 11.2 - - + -
54M ILE 3.7 7.0 - - - +
55M GLU* 4.1 25.1 - - + -
56M GLU 5.0 0.4 - - - +
64M LEU* 1.3 78.7 - - - +
66M LEU* 1.3 65.6 + - - +
67M ASP* 3.8 5.6 + - + +
99M GLN 3.7 1.6 - - - +
100M LEU* 4.6 2.5 - - - -
101M ILE* 2.8 54.8 + - + +
103M LYS* 3.7 35.9 - - + -
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Residues in contact with LEU 66 (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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52M PHE* 3.7 24.7 - - + -
53M PRO* 3.6 2.1 - - - +
54M ILE* 3.0 41.7 + - + +
64M LEU 4.2 1.0 - - - -
65M VAL* 1.3 71.9 - - - +
67M ASP* 1.3 59.8 + - - +
98M LEU* 4.1 16.6 - - + -
99M GLN 3.7 21.3 - - - +
100M LEU* 4.0 10.7 - - + +
355M VAL* 4.0 24.5 - - + -
359M MET* 5.0 1.9 - - - -
369M PRO* 4.2 13.5 - - + -
372M LEU* 4.2 19.1 - - + -
373M VAL* 4.2 22.9 - - + -
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Residues in contact with ASP 67 (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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52M PHE* 4.3 5.3 - - - +
53M PRO* 3.4 28.9 - - + +
65M VAL* 3.8 6.5 + - + +
66M LEU* 1.3 74.4 - - - +
68M PHE* 1.3 80.5 + - - +
69M LEU* 5.2 3.3 - - - +
98M LEU* 3.3 6.8 - - - +
99M GLN* 2.9 55.9 + - + +
101M ILE* 5.1 6.1 - - + +
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Residues in contact with PHE 68 (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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45M GLN* 3.3 29.6 - - - -
48M PHE* 3.5 48.5 - + + -
49M ARG* 4.3 15.3 - - - -
52M PHE* 3.5 27.8 - - + +
67M ASP* 1.3 87.1 + - - +
69M LEU* 1.3 71.8 + - - +
70M GLU* 3.2 35.9 - - - -
71M TYR* 3.9 10.1 - + + -
96M ALA* 4.9 0.7 - - + -
98M LEU* 3.5 22.0 - - + -
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Residues in contact with LEU 69 (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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45M GLN* 5.3 0.9 + - - -
67M ASP* 3.8 4.4 + - - +
68M PHE* 1.3 86.3 - - - +
70M GLU* 1.3 66.8 + - + +
97M ARG* 2.9 27.2 + - + +
98M LEU 4.6 2.2 - - - -
99M GLN* 3.7 39.3 - - + +
110M GLU* 3.2 39.5 - - + +
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Residues in contact with GLU 70 (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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36M PRO* 3.2 36.1 - - + +
37M GLU* 4.9 3.1 + - - +
39M ARG* 5.2 0.4 - - - +
45M GLN* 5.6 2.2 - - - +
68M PHE* 3.2 21.2 - - - -
69M LEU* 1.3 86.7 - - + +
71M TYR* 1.3 67.0 + - - +
96M ALA* 3.6 0.3 - - - -
97M ARG* 2.9 68.8 + - + +
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Residues in contact with TYR 71 (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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30M LEU 2.6 26.8 + - - -
31M GLN* 3.9 5.9 + - - +
36M PRO* 4.2 6.6 - - - +
39M ARG* 2.8 52.4 + - - +
44M ILE* 3.5 27.0 - - + +
45M GLN* 3.1 41.6 + - + -
48M PHE* 3.9 29.8 - + + -
68M PHE* 4.0 4.3 - + + -
70M GLU* 1.3 80.0 - - - +
72M ARG* 1.3 68.3 + - - +
73M LEU* 4.6 7.4 - - + -
94M LEU* 3.6 17.5 - - + -
95M TYR 3.4 12.8 - - - +
96M ALA* 4.2 2.7 - - - +
97M ARG* 4.6 1.1 - - - +
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Residues in contact with ARG 72 (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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36M PRO* 5.5 5.4 - - + -
39M ARG* 4.3 6.1 - - - +
71M TYR* 1.3 79.5 - - - +
73M LEU* 1.3 66.4 + - - +
74M GLY* 4.6 13.3 - - - -
93M PRO 3.8 0.3 - - - +
94M LEU* 3.4 7.1 - - - +
95M TYR* 2.9 79.5 + - + +
97M ARG* 6.3 1.1 - - + +
112M GLU* 3.0 30.0 + - - +
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Residues in contact with LEU 73 (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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30M LEU* 3.9 39.0 - - + +
32M ALA* 3.8 32.4 - - + +
39M ARG* 4.9 2.8 - - - +
44M ILE* 5.2 0.2 - - + -
71M TYR* 4.6 6.7 - - + -
72M ARG* 1.3 83.1 + - - +
74M GLY* 1.3 65.8 + - - +
75M GLU* 5.4 1.2 - - - +
92M ALA* 4.3 15.0 - - + +
93M PRO 3.4 4.5 - - - +
94M LEU* 3.6 33.2 - - + -
118M ILE* 4.5 14.8 - - + -
120M LEU* 5.2 4.0 - - + -
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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