Contacts of the strand formed by residues 73 - 79 (chain M) in PDB entry 5DSV
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 VAL 73 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68M ASN* 3.6 9.9 - - - +
69M VAL* 3.2 33.5 + - + -
70M ASP* 3.5 15.9 + - + +
71M ARG 3.4 0.6 - - - -
72M HIS* 1.3 112.5 - - + +
74M GLY* 1.3 69.3 + - - +
106M ILE* 4.9 1.8 - - + -
108M LEU* 3.7 33.2 - - + -
111M LEU* 4.1 18.2 - - + -
137M LEU* 4.3 6.1 - - + -
138M GLY 3.4 3.4 - - - +
139M SER* 4.2 0.4 - - - -
224M HIS* 4.0 4.9 - - - -
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Residues in contact with GLY 74 (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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47M PHE* 3.8 6.4 - - - -
67M PHE 3.4 6.7 - - - -
69M VAL 5.0 0.2 - - - -
73M VAL* 1.3 79.1 - - - +
75M MET* 1.3 59.8 + - - -
136M MET 3.5 0.7 - - - +
137M LEU* 3.2 6.4 - - - -
138M GLY 2.8 37.5 + - - -
224M HIS* 3.4 26.4 - - - -
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Residues in contact with MET 75 (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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47M PHE* 5.2 1.1 - - - -
65M ARG 3.8 0.5 - - - +
66M LEU* 3.3 7.7 - - - +
67M PHE* 2.9 40.4 + - + +
69M VAL* 3.7 30.2 - - + +
74M GLY* 1.3 74.1 - - - -
76M ALA* 1.3 64.0 + - - +
77M VAL* 3.7 26.7 - - + -
84M ALA* 3.9 9.4 - - - +
87M LEU* 4.3 5.4 - - + -
88M ALA* 3.8 34.3 - - + +
91M ALA* 4.9 2.9 - - - -
135M PHE* 3.7 27.4 - - + -
136M MET 3.2 4.7 - - - +
137M LEU* 3.8 16.6 - - + -
224M HIS* 4.7 0.5 + - - -
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Residues in contact with ALA 76 (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 ALA* 5.5 4.7 - - + -
37M ILE 5.5 1.1 - - - +
47M PHE* 3.5 28.5 - - + -
49M VAL* 5.2 2.7 - - + -
65M ARG 3.5 4.7 - - - -
66M LEU* 3.4 22.9 - - + -
75M MET* 1.3 75.0 - - - +
77M VAL* 1.3 59.8 + - - +
135M PHE* 3.1 2.8 - - - -
136M MET* 2.8 42.5 + - + +
165M ILE* 3.7 7.0 - - - +
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Residues in contact with VAL 77 (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 ALA* 4.2 6.4 - - - +
65M ARG* 3.1 46.0 + - + +
67M PHE* 3.8 26.7 - - + -
75M MET* 3.7 33.9 - - + -
76M ALA* 1.3 78.2 - - - +
78M ALA* 1.3 63.8 + - - +
81M LEU* 4.1 16.6 - - + -
84M ALA* 3.8 17.0 - - + -
134M SER 3.7 4.9 - - - +
135M PHE* 3.7 5.2 - - + -
165M ILE* 4.1 1.8 - - - -
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Residues in contact with ALA 78 (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 VAL* 3.8 13.8 - - + +
33M SER* 4.4 0.2 - - - +
34M SER 4.3 2.7 - - - +
36M ALA* 4.9 0.4 - - + -
65M ARG* 3.6 16.2 - - - +
77M VAL* 1.3 79.2 - - - +
79M GLY* 1.3 62.5 + - - +
84M ALA* 6.2 0.4 - - - -
133M CYS* 3.4 6.2 - - - +
134M SER 3.0 32.7 + - - +
165M ILE* 3.5 36.5 - - + +
166M GLY* 4.6 1.1 - - - +
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Residues in contact with GLY 79 (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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29M ALA 3.7 15.3 - - - -
30M VAL* 3.8 6.7 - - - +
33M SER* 3.1 35.9 + - - -
65M ARG* 5.7 1.0 - - - -
78M ALA* 1.3 74.0 - - - +
80M LEU* 1.3 64.9 + - - -
81M LEU* 3.2 9.5 + - - +
84M ALA* 6.2 0.2 - - - -
132M GLY 3.8 1.8 - - - -
133M CYS* 4.5 0.4 - - - -
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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