Contacts of the strand formed by residues 200 - 208 (chain M) in PDB entry 1V7M
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 SER 200 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196M THR* 4.5 4.7 - - - +
197M HIS 2.7 31.4 + - - +
198M LYS 3.3 3.8 + - - -
199M THR* 1.3 79.1 + - - +
201M THR* 1.3 60.8 + - - +
202M SER* 3.0 38.0 + - - +
204M ILE* 6.0 4.3 - - - -
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Residues in contact with THR 201 (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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196M THR* 4.9 8.7 - - - +
200M SER* 1.3 72.7 + - - +
202M SER* 1.3 61.1 + - - +
203M PRO* 3.7 8.0 - - - +
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Residues in contact with SER 202 (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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196M THR* 5.9 0.2 - - - -
200M SER* 3.0 27.4 + - - +
201M THR* 1.3 78.5 + - - +
203M PRO* 1.3 74.5 - - - +
204M ILE* 3.7 6.4 + - - +
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Residues in contact with PRO 203 (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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194M GLU* 4.1 22.2 - - + +
195M ALA 3.2 16.8 - - - +
196M THR* 3.4 22.4 - - + +
201M THR 3.7 6.9 - - - +
202M SER* 1.3 91.7 - - - +
204M ILE* 1.3 65.8 + - - +
205M VAL* 3.7 14.8 + - + +
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Residues in contact with ILE 204 (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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111M ALA* 5.7 5.8 - - + -
112M PRO* 4.5 22.9 - - + +
114M VAL* 3.4 35.5 - - + +
193M CYS 3.8 1.0 - - - +
194M GLU* 3.3 3.5 - - - -
195M ALA* 2.8 38.7 + - + +
200M SER* 6.0 3.8 - - - -
202M SER 4.7 5.2 - - - +
203M PRO* 1.3 74.5 - - - +
205M VAL* 1.3 65.7 + - - +
206M LYS* 4.9 2.5 - - + -
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Residues in contact with VAL 205 (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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192M THR* 3.6 27.4 - - + +
193M CYS 3.5 3.6 - - - -
194M GLU* 3.9 20.0 - - + +
203M PRO* 3.7 16.1 + - + +
204M ILE* 1.3 81.5 - - - +
206M LYS* 1.3 84.7 + - - +
207M SER* 5.1 2.9 - - - +
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Residues in contact with LYS 206 (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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114M VAL* 3.8 41.0 - - + +
115M SER* 4.9 2.0 - - - -
116M ILE* 3.5 25.1 - - + +
193M CYS* 2.9 33.5 + - + +
204M ILE* 4.9 3.6 - - + -
205M VAL* 1.3 88.5 + - - +
207M SER* 1.3 77.4 + - - +
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Residues in contact with SER 207 (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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116M ILE* 4.0 11.5 - - - +
190M SER* 5.7 0.9 - - - -
191M TYR 3.0 19.5 - - - -
192M THR* 3.1 20.7 + - - +
205M VAL* 5.1 3.3 - - - +
206M LYS* 1.3 88.8 + - - +
208M PHE* 1.3 68.2 + - - +
209M ASN* 5.6 3.7 + - - -
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Residues in contact with PHE 208 (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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130I GLY* 5.6 6.5 - - - -
116M ILE* 3.9 17.9 - - + -
118M PRO* 3.6 33.0 - - + -
131M VAL* 3.5 26.9 - - + -
185M TYR* 3.3 29.6 - + - -
189M ASN 3.6 2.1 - - - +
191M TYR* 3.3 62.1 + + + -
207M SER* 1.3 81.0 - - - +
209M ASN* 1.3 65.1 + - - +
210M ARG* 3.7 16.6 - - + +
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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