Contacts of the strand formed by residues 104 - 108 (chain G) in PDB entry 5MGS
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 LYS 104 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100G GLN* 3.5 7.1 - - - +
101G LEU* 2.9 36.3 + - + +
102G ARG 3.3 1.2 + - - -
103G GLU* 1.3 83.6 - - + +
105G CYS* 1.3 63.1 + - - +
106G LEU* 3.9 22.4 - - + -
130G LEU* 4.8 0.4 - - + -
131G LEU* 2.9 23.8 + - - +
133G ARG* 4.0 15.3 - - - +
137G GLU* 2.6 34.5 + - - +
211G GLN* 3.0 33.3 + - + +
212G LYS 3.5 7.9 - - - +
213G GLU* 4.7 14.1 - - + -
214G LEU* 4.5 0.7 - - - -
501G NAG 5.2 1.4 + - - -
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Residues in contact with CYS 105 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G LEU* 4.1 9.2 - - - -
94G CYS* 2.1 57.2 - - + -
95G PRO* 4.5 2.2 - - + -
98G TRP* 3.4 18.3 - - + -
99G GLN 3.5 1.3 - - - -
104G LYS* 1.3 72.3 - - - +
106G LEU* 1.3 61.2 + - - +
211G GLN* 3.2 5.5 - - - -
212G LYS* 2.8 45.1 + - + +
214G LEU* 3.7 23.8 - - - -
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Residues in contact with LEU 106 (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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97G TYR 4.4 0.2 - - - +
98G TRP* 3.4 4.0 - - - -
99G GLN* 2.8 40.7 + - + +
101G LEU* 4.1 28.7 - - + -
104G LYS* 3.9 18.6 - - + -
105G CYS* 1.3 82.7 - - - +
107G LEU* 1.4 59.6 - - - +
108G PHE* 3.9 33.0 + - + -
130G LEU* 3.8 24.0 - - + -
141G THR* 4.1 13.2 - - + +
144G LEU* 4.2 6.1 - - + -
209G ILE* 4.5 3.1 - - + -
210G CYS 3.3 4.3 - - - +
211G GLN* 3.9 11.9 - - + -
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Residues in contact with LEU 107 (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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97G TYR* 3.7 31.6 - - + +
98G TRP* 3.6 51.8 - - + +
106G LEU* 1.4 73.0 - - - +
108G PHE* 1.3 69.0 + - - +
109G SER* 3.7 3.0 + - - +
121G ASP* 5.5 0.2 - - - +
125G LYS* 3.8 28.5 - - + -
208G TRP* 3.6 2.2 - - - +
209G ILE* 3.3 5.7 - - - -
210G CYS* 2.9 37.6 + - + +
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Residues in contact with PHE 108 (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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97G TYR 5.5 1.0 + - - -
99G GLN* 3.5 28.1 + - - +
106G LEU* 3.9 35.9 - - + -
107G LEU* 1.3 81.8 - - - +
109G SER* 1.4 65.0 + - - +
110G HIS* 3.8 3.6 + - - +
141G THR* 4.2 7.2 - - + -
144G LEU* 4.0 30.5 - - + -
145G ILE* 4.1 20.0 - - + -
152G PHE* 3.9 24.7 - + + -
208G TRP 3.9 3.1 - - - -
209G ILE* 3.4 33.7 - - + -
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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