Contacts of the strand formed by residues 207 - 213 (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 ARG 207 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109G SER* 3.2 22.9 + - - +
110G HIS* 3.8 20.6 + - - +
111G THR 3.4 17.3 - - - +
112G VAL* 3.9 16.2 - - + +
150G ILE* 3.7 38.3 - - - +
151G LEU 3.5 7.2 + - - +
152G PHE* 3.3 22.5 - - + -
153G TRP* 2.9 19.7 + - - -
206G ILE* 1.3 86.2 - - - +
208G TRP* 1.3 62.9 + - - +
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Residues in contact with TRP 208 (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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107G LEU* 3.6 1.7 - - - +
108G PHE* 3.8 1.4 - - - -
109G SER* 2.9 56.5 + - - -
111G THR* 3.2 35.7 - - - -
112G VAL 3.8 3.8 - - - -
113G ASN* 3.3 33.4 - - + -
118G SER* 3.5 34.8 - - - +
121G ASP* 2.9 44.6 + - + +
122G CYS* 3.8 8.3 - - - -
125G LYS* 5.6 0.7 - - - -
129G LEU* 4.1 1.6 - - + -
152G PHE* 3.7 1.8 - - - -
153G TRP* 3.7 17.3 - - + +
206G ILE 3.9 1.6 - - - -
207G ARG* 1.3 78.7 - - - +
209G ILE* 1.3 64.7 + - - +
210G CYS* 3.6 22.8 - - - -
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Residues in contact with ILE 209 (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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106G LEU* 4.5 13.0 - - + -
107G LEU 3.3 8.1 - - - +
108G PHE* 3.4 38.4 - - + -
122G CYS* 4.3 0.4 - - - -
129G LEU* 3.6 9.0 - - - +
130G LEU* 2.9 55.3 + - + +
141G THR* 4.6 0.4 - - + -
152G PHE* 3.6 26.2 - - + -
153G TRP 3.2 8.3 + - - +
154G ILE* 4.7 0.2 - - + -
192G ILE* 3.9 23.6 - - + -
208G TRP* 1.3 77.1 - - - +
210G CYS* 1.3 73.9 + - - +
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Residues in contact with CYS 210 (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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98G TRP* 3.8 13.2 - - + -
106G LEU* 3.3 5.2 - - - -
107G LEU* 2.9 38.8 + - + -
121G ASP* 3.9 5.2 - - - -
122G CYS* 2.1 50.5 - - - -
125G LYS* 4.8 5.6 - - - -
127G SER* 3.4 13.7 - - - +
128G SER 3.2 4.5 - - - -
130G LEU 4.8 0.2 - - - -
208G TRP* 3.6 16.8 - - - -
209G ILE* 1.3 78.2 - - - +
211G GLN* 1.3 60.1 + - - +
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Residues in contact with GLN 211 (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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98G TRP* 3.9 2.2 - - - -
104G LYS* 3.0 36.8 + - + +
105G CYS 3.2 7.4 - - - +
106G LEU* 3.9 13.2 - - + -
127G SER* 3.3 5.2 - - - -
128G SER* 2.6 51.1 + - - +
129G LEU 4.0 3.8 - - - +
130G LEU* 3.6 5.9 - - + +
131G LEU* 2.8 44.4 + - - +
210G CYS* 1.3 74.8 - - - +
212G LYS* 1.3 62.0 + - - +
213G GLU* 4.0 21.8 + - - +
126H GLU* 4.3 3.9 + - - +
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Residues in contact with LYS 212 (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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91G LEU* 3.7 31.3 - - + +
95G PRO* 4.7 12.6 - - + -
98G TRP* 3.7 32.5 - - + -
104G LYS* 3.5 2.9 - - - -
105G CYS* 2.8 44.5 + - + +
125G LYS 3.1 18.8 + - - -
126G GLU* 2.8 38.2 + - - +
127G SER* 4.1 0.7 - - - -
211G GLN* 1.3 78.9 - - - +
213G GLU* 1.3 61.4 + - - +
214G LEU 3.6 0.5 + - - -
126H GLU* 3.4 13.0 + - - +
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Residues in contact with GLU 213 (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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91G LEU* 3.1 18.2 - - - +
103G GLU 3.6 6.1 - - - +
104G LYS* 4.6 13.9 - - + +
131G LEU* 5.5 3.6 - - - +
211G GLN* 4.0 21.7 + - - +
212G LYS* 1.3 69.5 - - - +
214G LEU* 1.3 64.9 + - - +
126H GLU* 2.7 24.9 + - - +
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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