Contacts of the strand formed by residues 66 - 71 (chain G) in PDB entry 6S1M
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 66 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2G PHE* 3.5 33.4 - - + +
28G TRP 4.1 0.2 - - - -
29G ASP* 3.4 4.7 - - - +
30G ILE* 2.8 48.1 + - + +
64G ARG* 3.2 11.7 + - + +
65G ASN* 1.3 74.9 - - - +
67G ALA* 1.3 64.8 + - - +
68G MET* 4.0 18.6 - - + -
92G ALA* 3.8 17.9 - - + -
93G GLU 4.9 3.1 - - - +
94G ASP* 4.2 34.3 - - + +
96G ALA 5.8 1.3 - - - +
118G LEU* 6.1 2.0 - - + -
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Residues in contact with ALA 67 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27G CYS* 4.1 19.7 - - - -
28G TRP 3.6 3.6 - - - -
29G ASP* 4.2 6.7 - - - +
66G LEU* 1.3 79.3 - - - +
68G MET* 1.3 62.4 + - - +
69G GLY 3.7 2.8 + - - -
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Residues in contact with MET 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G PHE* 4.0 20.4 - - + -
27G CYS* 4.2 1.1 - - - -
28G TRP* 2.9 39.0 + - + +
30G ILE* 3.2 39.3 - - + -
66G LEU* 4.0 20.4 - - + -
67G ALA* 1.3 72.7 - - - +
69G GLY* 1.3 61.6 + - - +
70G VAL* 2.9 23.0 + - + +
90G LEU* 6.2 0.2 - - + -
92G ALA* 4.2 6.5 - - + -
99G LEU* 4.0 37.7 - - + -
118G LEU* 3.8 23.1 - - + -
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Residues in contact with GLY 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ALA 3.5 1.6 - - - -
27G CYS* 4.3 5.3 - - - -
67G ALA 3.7 4.9 + - - -
68G MET* 1.3 68.7 - - - +
70G VAL* 1.3 58.5 + - - -
118G LEU* 3.8 7.5 - - - +
119G MET* 3.0 44.0 + - - +
121G LEU* 3.2 29.4 - - - -
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Residues in contact with VAL 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G GLU* 3.4 2.9 - - - +
26G ALA* 2.6 39.7 + - - +
28G TRP* 3.4 26.9 - - + +
68G MET* 2.9 28.1 + - + +
69G GLY* 1.3 74.8 - - - -
71G ASN* 1.3 74.6 + - - +
72G LEU* 3.3 4.3 + - + +
75G MET* 3.8 18.6 - - + -
99G LEU* 5.1 4.5 - - + -
116G MET* 3.6 27.6 - - + -
117G LYS 5.9 0.4 - - - -
118G LEU* 4.0 11.9 - - + +
119G MET* 4.9 1.8 - - - -
121G LEU* 4.7 0.9 - - - -
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Residues in contact with ASN 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ASN* 3.0 20.7 + - - +
25G GLU* 4.4 10.6 - - - +
69G GLY 4.2 0.8 + - - -
70G VAL* 1.3 74.3 - - - +
72G LEU* 1.3 62.1 + - - +
73G THR* 3.1 20.6 + - - +
74G SER* 3.0 27.9 + - - +
75G MET* 3.0 21.5 + - - +
116G MET* 4.8 1.6 - - + +
117G LYS 5.6 5.0 + - - +
119G MET* 4.2 25.3 - - + +
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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