Contacts of the helix formed by residues 2433 - 2443 (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 LYS2433 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2333B GLY 4.6 0.7 - - - +
2334B ARG* 3.2 23.1 - - - +
2335B THR 4.0 10.8 + - - +
2336B GLY* 3.7 17.9 - - - -
2424B ARG* 5.5 1.8 - - - +
2425B CYS* 2.6 31.3 + - - -
2426B PRO* 4.1 5.7 - - - +
2427B ASN 3.5 23.7 + - - +
2428B PRO* 4.6 10.5 - - + +
2430B CYS* 3.2 25.6 - - + +
2431B PRO 2.8 2.6 + - - -
2432B ALA* 1.3 76.4 - - - +
2434B ARG* 1.3 59.1 + - - +
2435B PHE 3.3 2.5 - - - -
2436B GLU* 3.4 3.4 + - + -
2437B ALA* 2.8 33.6 + - + +
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Residues in contact with ARG2434 (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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2429B LEU 5.0 6.0 + - - +
2430B CYS 3.7 4.2 + - - +
2431B PRO* 2.9 52.2 + - + +
2432B ALA 3.6 0.8 - - - -
2433B LYS* 1.3 77.5 - - - +
2435B PHE* 1.3 62.4 + - - +
2437B ALA* 3.0 7.5 + - - +
2438B ILE* 2.9 30.6 + - - +
2461B LEU* 4.1 21.5 - - + -
2466B VAL 5.6 0.2 - - - -
2467B ARG* 3.2 60.1 + - - +
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Residues in contact with PHE2435 (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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2334B ARG* 5.8 7.9 - - + -
2433B LYS 3.3 0.6 - - - -
2434B ARG* 1.3 78.2 - - - +
2436B GLU* 1.3 72.9 + - + +
2437B ALA 3.0 0.5 + - - -
2438B ILE* 3.3 0.7 + - - +
2439B ARG* 3.1 51.5 + - + +
2454B GLU* 3.5 42.8 - - + -
2457B ILE* 4.3 13.3 - - + +
2458B GLU* 3.6 49.8 - - + -
2461B LEU* 4.7 6.4 - - + +
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Residues in contact with GLU2436 (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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2334B ARG* 3.0 50.3 - - + +
2335B THR* 4.7 7.6 - - - -
2433B LYS* 3.4 3.6 + - - +
2435B PHE* 1.3 83.9 - - - +
2437B ALA* 1.3 60.4 + - - +
2439B ARG* 4.0 27.9 + - - -
2440B HIS* 3.3 37.4 + - + +
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Residues in contact with ALA2437 (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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2428B PRO 5.3 8.1 - - - +
2433B LYS* 2.8 22.1 + - + +
2434B ARG* 3.1 11.0 - - - +
2435B PHE 2.9 1.2 - - - -
2436B GLU* 1.3 76.9 - - - +
2438B ILE* 1.3 69.9 + - + +
2440B HIS* 3.9 3.3 - - - +
2441B TYR* 3.1 20.8 + - - +
2467B ARG 6.0 0.4 - - - +
2468B ASP* 6.0 2.0 - - - -
2469B VAL* 4.2 9.1 - - + +
2512B ALA 4.7 2.9 - - - +
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Residues in contact with ILE2438 (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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2434B ARG 2.9 20.7 + - - +
2437B ALA* 1.3 69.9 - - + +
2439B ARG* 1.3 59.8 + - - +
2441B TYR* 2.5 30.8 + - - +
2442B ALA* 2.9 10.6 + - - +
2452B LEU* 3.7 20.0 - - + -
2457B ILE* 3.6 36.6 - - + -
2460B LEU* 6.2 0.2 - - + -
2461B LEU* 4.7 4.0 - - + -
2466B VAL* 3.7 19.7 - - + -
2467B ARG 4.6 2.5 - - - +
2468B ASP* 3.6 34.5 - - - -
2469B VAL* 3.9 4.9 - - - +
2472B LEU* 3.8 16.2 - - + -
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Residues in contact with ARG2439 (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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2334B ARG* 6.3 0.6 - - - +
2435B PHE* 3.1 40.5 + - + +
2436B GLU* 4.0 21.2 + - - +
2438B ILE* 1.3 78.5 - - - +
2440B HIS* 1.3 55.9 + - - +
2442B ALA* 3.1 4.0 + - - +
2443B SER* 2.7 35.4 + - - -
2452B LEU 6.1 0.2 - - - +
2454B GLU* 4.1 30.4 + - + +
2457B ILE* 3.5 19.2 - - + +
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Residues in contact with HIS2440 (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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2436B GLU* 3.3 32.6 + - - +
2437B ALA* 3.9 3.1 - - - +
2438B ILE 3.2 0.8 - - - -
2439B ARG* 1.3 81.0 - - - +
2441B TYR* 1.3 58.5 + - - +
2443B SER* 3.4 11.1 + - - -
2446B ALA* 2.7 22.1 - - + +
2511B TYR* 3.0 60.9 + + - -
2512B ALA 4.3 6.7 - - - +
2514B GLY* 5.1 10.3 - - - -
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Residues in contact with TYR2441 (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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2437B ALA 3.1 7.2 + - - +
2438B ILE* 2.5 19.6 + - - +
2440B HIS* 1.3 73.0 - - - +
2442B ALA* 1.3 53.9 + - - -
2446B ALA* 3.1 1.1 - - - +
2447B MET* 2.9 63.7 + - + +
2449B ILE* 4.6 7.0 - - + -
2469B VAL* 3.3 45.5 - - + -
2472B LEU* 4.1 14.1 - - + -
2473B TYR* 2.8 42.7 + + - -
2509B LEU* 4.0 12.4 - - + +
2512B ALA* 3.6 27.6 + - + +
2513B LEU* 4.6 3.4 - - + -
2574B LEU* 4.2 6.4 - - + +
2579B VAL* 3.9 18.4 - - - +
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Residues in contact with ALA2442 (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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2438B ILE 2.9 8.9 + - - +
2439B ARG* 3.8 8.3 - - - +
2441B TYR* 1.3 73.7 - - + +
2443B SER* 1.3 72.0 + - - +
2448B ASP* 3.2 0.3 - - - +
2449B ILE* 2.7 56.3 + - + +
2450B GLU* 4.3 1.0 + - - -
2452B LEU* 4.2 27.8 - - + +
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Residues in contact with SER2443 (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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2439B ARG* 2.7 19.7 + - - -
2440B HIS* 3.4 19.7 + - - -
2441B TYR 3.3 0.6 - - - -
2442B ALA* 1.3 85.4 - - - +
2444B ARG* 1.3 61.4 + - - +
2445B LYS* 3.7 4.3 + - - +
2446B ALA* 3.1 25.3 + - - +
2448B ASP 2.9 16.5 + - - -
2511B TYR* 4.7 2.8 + - - -
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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