Contacts of the strand formed by residues 154 - 157 (chain I) 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 THR 154 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I PRO* 5.6 6.7 - - + -
153I VAL* 1.3 81.5 - - - +
155I VAL* 1.3 62.4 + - - +
156I THR* 6.0 2.0 - - - -
180I LEU* 6.3 0.2 - - - -
199I ASN 3.7 0.4 - - - +
200I VAL* 3.6 4.5 - - - -
201I ALA* 2.9 48.9 + - - +
203I PRO* 5.4 4.5 - - + +
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Residues in contact with VAL 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143I CYS* 4.9 2.7 - - + -
145I VAL* 5.6 1.3 - - + -
153I VAL* 4.5 0.9 + - + -
154I THR* 1.3 75.4 - - - +
156I THR* 1.3 77.8 + - - +
157I TRP* 4.9 4.1 - - + +
166I VAL* 6.0 1.6 - - + +
168I THR* 3.0 44.3 + - + +
180I LEU* 5.0 8.5 - - + -
182I SER* 3.7 18.6 - - - +
198I CYS* 4.3 10.5 - - + -
199I ASN 3.4 8.5 - - - +
200I VAL* 4.1 17.7 - - + -
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Residues in contact with THR 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I THR* 6.0 2.7 - - - -
155I VAL* 1.3 80.0 - - - +
157I TRP* 1.3 67.5 + - - +
159I SER* 4.1 2.9 - - - -
160I GLY* 3.9 19.6 + - - +
198I CYS* 3.1 10.2 - - - +
199I ASN* 2.6 58.5 + - - +
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Residues in contact with TRP 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I LEU* 4.9 1.8 - - + -
142I GLY* 3.3 34.3 - - - -
143I CYS* 3.8 10.1 - - + -
155I VAL* 4.9 3.9 - - + +
156I THR* 1.3 78.3 + - - +
158I ASN* 1.3 68.5 + - - +
159I SER 3.3 1.3 - - - -
160I GLY* 2.8 11.4 + - - -
162I LEU* 3.2 41.1 + - + +
166I VAL* 3.7 26.2 - - + +
182I SER* 3.1 43.1 + - - -
183I SER 4.0 7.3 + - - -
184I VAL* 3.8 24.0 - - + -
196I VAL* 3.8 20.2 - - + -
197I THR 3.2 7.9 - - - +
198I CYS* 3.5 36.3 - - + -
210I ASP 5.6 0.4 - - - -
212I LYS* 5.2 4.9 - - + -
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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