Contacts of the strand formed by residues 2353 - 2358 (chain B) in PDB entry 1V9P
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 GLU2353 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2346B PRO* 4.1 29.9 - - + +
2347B VAL 3.3 10.3 - - - +
2348B PHE* 4.4 18.0 - - + +
2352B SER* 1.3 78.9 - - - +
2354B VAL* 1.3 74.3 + - - +
2355B SER* 4.2 15.3 + - - -
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Residues in contact with VAL2354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2344B LEU* 4.3 18.8 - - + +
2345B GLU 4.1 4.0 - - - +
2347B VAL* 2.6 41.5 + - + +
2349B ILE* 4.1 28.3 - - + +
2352B SER* 4.7 2.0 - - - +
2353B GLU* 1.3 82.9 - - - +
2355B SER* 1.3 62.4 + - - +
2356B ARG 3.8 18.8 - - - +
2357B VAL* 5.0 0.4 - - + -
2378B VAL* 4.9 4.0 - - + -
2380B LYS* 4.8 5.8 - - - -
2386B PRO* 4.2 25.8 - - + -
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Residues in contact with SER2355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2343B VAL* 3.8 2.6 - - - +
2344B LEU* 2.8 40.0 + - - +
2346B PRO* 5.2 7.2 - - - -
2353B GLU* 4.2 16.0 - - - +
2354B VAL* 1.3 73.2 - - - +
2356B ARG* 1.3 86.5 + - - +
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Residues in contact with ARG2356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2329B VAL* 5.3 5.3 - - - +
2341B VAL* 4.4 21.1 - - + -
2342B GLY 3.8 3.6 - - - -
2343B VAL* 4.3 26.6 - - + +
2354B VAL* 3.8 13.1 - - - +
2355B SER* 1.3 99.3 + - - +
2357B VAL* 1.3 60.6 + - - +
2386B PRO* 4.5 6.9 - - - +
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Residues in contact with VAL2357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2325B LEU* 5.2 0.4 - - + -
2341B VAL* 3.4 8.0 - - - +
2342B GLY* 2.9 43.8 + - - +
2344B LEU* 3.3 34.8 - - + -
2354B VAL* 5.0 1.6 - - + -
2356B ARG* 1.3 75.7 - - - +
2358B THR* 1.3 70.3 + - - +
2359B LEU* 5.1 6.7 - - + -
2378B VAL* 4.4 3.4 - - + -
2386B PRO* 3.5 7.9 - - - +
2387B GLU* 3.1 36.1 - - - +
2388B VAL* 3.7 9.9 - - + +
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Residues in contact with THR2358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2190B GLU* 4.4 5.4 + - - -
2339B THR* 4.7 2.8 - - - +
2340B PRO 3.9 11.4 + - - -
2341B VAL* 4.4 5.6 - - - +
2357B VAL* 1.3 87.1 - - - +
2359B LEU* 1.3 66.3 + - - +
2360B HIS* 3.0 39.6 + - + +
2364B TYR* 5.2 0.5 - - - -
2385B ILE* 4.3 13.7 - - + -
2386B PRO 4.2 13.4 + - - +
2387B GLU* 4.1 7.6 - - - +
2388B VAL* 4.5 2.3 - - - +
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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