Contacts of the strand formed by residues 2388 - 2393 (chain B) in PDB entry 2NVU
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 LYS2388 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2384B THR* 3.5 5.0 - - - -
2385B LEU 3.0 27.8 + - - +
2386B GLU* 3.8 11.6 - - + +
2387B GLY* 1.3 83.4 - - - +
2389B ASN* 1.3 63.6 + - - +
2390B ARG* 3.1 32.3 + - - +
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Residues in contact with ASN2389 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2383B ALA 3.8 4.7 - - - +
2384B THR* 4.1 12.6 + - - +
2388B LYS* 1.3 72.4 - - - +
2390B ARG* 1.3 77.4 + - - +
27C ALA* 4.7 3.1 - - - +
28C SER 5.2 0.2 + - - -
31C GLN* 2.9 55.3 + - - +
55C ASP* 3.6 23.4 - - - +
56C ASP* 5.9 0.2 - - - -
58C LEU* 4.5 15.0 - - - +
84C GLN* 5.8 1.2 + - - -
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Residues in contact with ARG2390 (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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2382B THR* 3.2 7.2 - - - -
2383B ALA 2.8 40.6 + - - +
2385B LEU* 3.6 45.4 + - + +
2386B GLU* 4.8 6.3 - - - +
2388B LYS* 3.1 34.7 - - - +
2389B ASN* 1.3 94.2 + - - +
2391B THR* 1.3 64.8 + - - +
2392B LEU* 3.4 11.4 + - + +
55C ASP* 3.2 27.9 + - - +
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Residues in contact with THR2391 (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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2381B ILE 4.0 5.4 - - - +
2382B THR* 4.3 8.2 - - + +
2390B ARG* 1.3 71.4 - - - +
2392B LEU* 1.3 61.7 + - - +
2393B TYR 4.0 7.4 - - - +
2394B LEU* 3.9 31.4 - - + -
2400B ILE* 4.2 2.7 - - + -
2404B THR* 3.3 22.1 - - + +
2407B ASN* 3.8 3.8 + - - -
54C PRO 2.9 29.2 + - - +
55C ASP* 2.9 19.8 + - - +
57C LEU* 3.7 19.9 - - + +
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Residues in contact with LEU2392 (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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2361B LEU* 4.2 19.5 - - + +
2381B ILE* 2.9 38.1 + - + +
2382B THR* 4.2 1.3 - - - -
2383B ALA* 3.9 18.4 - - + -
2385B LEU* 4.6 19.5 - - + -
2390B ARG* 3.4 15.7 + - + +
2391B THR* 1.3 74.3 - - - +
2393B TYR* 1.3 63.4 + - - +
2404B THR* 3.3 5.0 - - - +
2407B ASN* 2.8 33.5 + - - +
2415B LEU* 4.7 24.7 - - + +
2417B LEU* 4.6 6.7 - - + -
2423B LEU* 4.0 12.1 - - + -
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Residues in contact with TYR2393 (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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2361B LEU* 5.0 2.0 - - + -
2365B LEU* 3.9 28.5 - - + -
2379B PRO 4.5 0.7 - - - -
2380B ALA* 3.4 4.2 - - - +
2381B ILE* 2.8 36.3 + - + +
2382B THR* 5.7 0.2 - - - +
2391B THR* 3.5 2.2 - - - +
2392B LEU* 1.3 81.2 - - + +
2394B LEU* 1.3 64.9 + - - +
2395B GLN* 3.4 42.6 + - + +
2401B GLU* 2.7 27.2 + - - -
2404B THR* 3.6 21.5 - - - -
2405B ARG* 3.6 29.0 + - - +
2408B LEU* 3.7 32.1 - - + +
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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