Contacts of the helix formed by residues 2519 - 2536 (chain B) in PDB entry 1CVU
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 GLY2519 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2435B ALA* 3.8 8.2 - - - +
2507B LEU 5.5 0.4 + - - -
2510B GLU* 3.3 18.6 + - - -
2511B LYS 3.6 20.2 - - - -
2512B PRO* 4.0 1.1 - - - -
2513B ARG* 4.2 5.6 - - - -
2518B PHE* 1.3 77.8 - - - +
2520B GLU* 1.3 67.3 + - - +
2522B MET* 3.3 12.1 + - - +
2523B VAL* 3.5 10.7 + - - +
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Residues in contact with GLU2520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2085B THR* 5.8 0.2 - - - -
2086B PRO* 3.6 26.0 - - - +
2087B ASN* 4.0 19.3 + - - +
2467B ARG* 2.7 36.7 + - - +
2472B LEU* 3.6 11.0 - - + +
2473B LYS 5.4 0.3 + - - -
2475B TYR* 4.3 5.0 + - - +
2510B GLU* 3.6 7.8 + - - +
2511B LYS 4.7 1.2 + - - -
2513B ARG* 3.1 36.3 - - - +
2519B GLY* 1.3 70.3 - - - -
2521B THR* 1.3 64.0 + - - +
2523B VAL* 3.2 3.1 + - - +
2524B GLU* 3.0 31.7 + - + +
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Residues in contact with THR2521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2463B LEU* 4.2 12.2 - - + +
2467B ARG* 2.7 37.1 + - + +
2472B LEU* 4.2 8.7 - - - -
2475B TYR* 4.3 1.6 - - - -
2503B LEU* 4.2 13.5 - - + -
2507B LEU* 3.6 17.7 - - + -
2510B GLU* 2.8 20.6 + - - -
2520B GLU* 1.3 77.4 - - - +
2522B MET* 1.3 63.5 + - - +
2525B LEU* 3.1 41.9 + - + +
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Residues in contact with MET2522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2384B LEU* 3.3 33.9 - - + +
2387B TRP* 3.1 37.9 - - + +
2434B VAL* 4.0 11.2 - - + -
2507B LEU* 3.5 35.7 - - + +
2508B LEU* 4.9 2.0 - - + -
2510B GLU* 4.0 2.1 + - - +
2518B PHE* 3.6 41.3 - - + -
2519B GLY 3.3 11.1 + - - +
2520B GLU 3.3 0.6 - - - -
2521B THR* 1.3 76.7 - - - +
2523B VAL* 1.3 63.4 + - - +
2525B LEU* 4.4 1.4 - - - +
2526B GLY* 3.0 22.7 + - - -
2701B ACD 3.9 3.3 - - + +
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Residues in contact with VAL2523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2090B HIS* 6.1 1.1 - - + +
2120B ARG* 4.4 3.6 - - - +
2352B LEU 6.1 0.7 - - - +
2355B TYR* 4.7 5.2 - - - +
2513B ARG* 4.0 21.5 - - - +
2518B PHE* 4.1 17.0 - - + -
2519B GLY 3.5 11.9 + - - +
2520B GLU 3.2 6.3 + - - +
2522B MET* 1.3 76.7 - - - +
2524B GLU* 1.3 72.2 + - - +
2527B ALA* 3.0 30.8 + - - +
2701B ACD 3.9 48.0 - - + +
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Residues in contact with GLU2524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2086B PRO* 3.7 30.9 - - + +
2120B ARG* 3.1 33.7 + - - +
2123B LEU* 5.6 0.7 - - - +
2470B PHE* 3.6 11.7 - - - +
2472B LEU* 3.6 37.0 - - + +
2513B ARG* 4.6 4.2 + - - +
2520B GLU* 3.0 22.7 + - + +
2523B VAL* 1.3 85.5 - - - +
2525B LEU* 1.3 58.3 + - + +
2527B ALA* 5.0 0.7 - - - -
2528B PRO* 3.1 22.5 - - - +
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Residues in contact with LEU2525 (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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2380B GLU* 5.6 2.5 - - + -
2384B LEU* 4.0 15.9 - - + -
2466B TYR* 4.1 26.9 - - + +
2470B PHE* 3.4 53.0 - - + -
2472B LEU* 4.0 13.2 - - + -
2503B LEU* 4.3 17.0 - - + -
2507B LEU* 5.6 1.1 - - + -
2521B THR* 3.1 31.2 + - + +
2522B MET* 4.4 0.7 - - - +
2524B GLU* 1.3 77.4 - - - +
2526B GLY* 1.3 63.9 + - - +
2527B ALA 3.5 0.2 - - - -
2528B PRO* 3.2 9.7 - - - +
2529B PHE* 2.9 29.7 - - + -
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Residues in contact with GLY2526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2381B PHE* 3.8 3.9 - - - -
2384B LEU* 3.9 13.6 - - - +
2522B MET 3.0 10.2 + - - -
2525B LEU* 1.3 77.5 - - - +
2527B ALA* 1.3 57.7 + - - +
2529B PHE* 3.2 5.0 + - - +
2530B SER* 2.9 31.0 + - - -
2701B ACD 3.5 27.4 - - - -
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Residues in contact with ALA2527 (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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2120B ARG* 3.7 32.1 - - - +
2523B VAL 3.0 18.9 + - - +
2526B GLY* 1.3 75.5 - - - +
2528B PRO* 1.3 63.1 - - + +
2530B SER* 3.2 7.0 + - - -
2531B LEU* 2.9 30.3 + - - +
2701B ACD 3.7 31.7 - - + +
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Residues in contact with PRO2528 (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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2120B ARG* 4.3 21.5 - - + +
2123B LEU* 4.0 22.0 - - + -
2124B ILE* 3.7 23.1 - - + +
2470B PHE* 4.0 10.8 - - + -
2524B GLU 3.1 25.8 - - - +
2525B LEU 3.2 9.4 - - - +
2527B ALA* 1.3 95.7 - - + +
2529B PHE* 1.3 60.1 + - - +
2531B LEU* 4.0 2.9 - - + +
2532B LYS* 3.3 28.8 + - - +
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Residues in contact with PHE2529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2124B ILE* 3.3 30.3 - - + -
2151B ALA* 3.9 15.5 - - + -
2375B ASN* 4.6 3.3 + - - +
2378B ALA* 3.4 31.2 - - + -
2380B GLU* 4.2 8.5 - - + -
2381B PHE* 3.4 50.1 - + + -
2384B LEU* 3.9 14.4 - - + -
2470B PHE* 3.8 20.0 - + - -
2525B LEU* 2.9 29.2 - - + -
2526B GLY 3.2 2.3 + - - +
2528B PRO* 1.3 79.2 - - - +
2530B SER* 1.3 61.6 + - - +
2532B LYS* 3.6 4.2 + - - +
2533B GLY* 3.1 18.4 + - - -
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Residues in contact with SER2530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2349B VAL* 4.6 3.0 - - - +
2381B PHE* 4.0 6.0 - - - -
2526B GLY 2.9 16.7 + - - -
2527B ALA* 3.5 6.5 - - - -
2529B PHE* 1.3 76.0 - - - +
2531B LEU* 1.3 61.2 + - - +
2533B GLY* 3.1 3.1 + - - -
2534B LEU* 2.8 43.9 + - - +
2701B ACD 2.6 52.2 + - - +
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Residues in contact with LEU2531 (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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2117B LEU* 3.4 44.4 - - + +
2120B ARG* 3.5 20.4 - - + -
2121B SER* 4.0 12.3 - - - +
2366B LEU* 4.8 2.2 - - + -
2371B PHE* 4.3 13.9 - - + -
2527B ALA 2.9 16.0 + - - +
2528B PRO* 4.0 4.9 - - + +
2530B SER* 1.3 75.5 + - - +
2532B LYS* 1.3 61.4 + - + +
2534B LEU* 4.6 0.4 - - - -
2535B MET* 2.7 65.2 + - + +
2701B ACD 4.2 20.2 - - + +
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Residues in contact with LYS2532 (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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2121B SER 6.0 1.8 - - - +
2124B ILE* 4.1 28.9 - - + +
2126B SER* 3.1 27.2 + - - -
2371B PHE* 4.0 16.1 - - + -
2372B GLN* 2.9 33.9 + - - +
2374B GLN 2.9 20.0 + - - +
2375B ASN* 3.4 24.9 - - - +
2528B PRO 3.3 17.5 + - - +
2529B PHE* 3.8 4.0 - - - +
2530B SER 3.2 0.8 - - - -
2531B LEU* 1.3 84.3 - - + +
2533B GLY* 1.3 58.7 - - - +
2536B GLY* 3.0 27.6 + - - +
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Residues in contact with GLY2533 (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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2227B GLY* 4.9 4.2 - - - -
2228B VAL* 3.8 23.2 + - - +
2375B ASN* 3.6 20.5 - - - +
2381B PHE* 6.3 0.9 - - - -
2529B PHE 3.1 11.3 + - - -
2530B SER* 3.1 7.0 + - - -
2532B LYS* 1.3 77.5 - - - +
2534B LEU* 1.3 64.5 + - - +
2537B ASN* 4.4 8.7 + - - +
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Residues in contact with LEU2534 (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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2205B PHE* 4.1 14.4 - - + -
2228B VAL* 3.8 23.8 - - + -
2341B ILE* 3.7 29.3 - - + +
2344B VAL* 3.8 18.2 - - + -
2345B ILE* 4.2 24.7 - - + -
2349B VAL* 5.0 1.6 - - + -
2530B SER* 2.8 40.1 + - - +
2531B LEU* 4.0 2.5 - - - +
2533B GLY* 1.3 77.4 - - - +
2535B MET* 1.3 67.3 + - + +
2536B GLY 3.3 0.6 + - - -
2537B ASN* 3.5 18.7 - - - +
2540B CYS* 3.6 8.0 - - - -
2701B ACD 3.6 14.6 - - + +
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Residues in contact with MET2535 (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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2117B LEU* 4.7 7.9 - - + -
2345B ILE* 4.0 24.5 - - - -
2360B LYS 5.8 0.9 - - - +
2361B PHE* 4.0 15.0 - - + -
2362B ASP 4.0 8.5 - - - +
2363B PRO* 3.6 37.0 - - + -
2366B LEU* 3.7 25.6 - - + -
2371B PHE* 3.7 4.0 - - + -
2373B TYR* 3.3 12.2 - - + -
2531B LEU* 2.7 43.7 + - + +
2534B LEU* 1.3 69.2 - - - +
2536B GLY* 1.3 55.4 + - - -
2537B ASN 3.1 5.5 + - - -
2540B CYS* 3.2 25.5 - - + +
2701B ACD 4.0 9.6 - - + -
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Residues in contact with GLY2536 (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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2371B PHE* 3.8 15.8 - - - -
2372B GLN 4.3 0.9 - - - -
2373B TYR* 3.3 27.2 - - - +
2374B GLN* 3.4 10.5 + - - -
2375B ASN* 4.9 1.7 + - - -
2531B LEU 3.7 1.2 + - - -
2532B LYS* 3.0 22.8 + - - -
2533B GLY 5.0 0.4 - - - -
2535B MET* 1.3 76.2 - - - +
2537B ASN* 1.3 62.7 + - - +
2538B PRO* 3.6 3.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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