Contacts of the helix formed by residues 2417 - 2429 (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 HIS2417 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2397B ILE* 3.4 34.7 + - + +
2398B GLU* 3.0 38.4 - - + +
2400B GLN* 3.8 10.0 - - + +
2402B TYR* 2.8 34.0 + + - -
2413B ILE* 2.9 26.2 + - - +
2415B LEU 4.5 0.2 - - - -
2416B GLU* 1.3 92.7 + - - +
2418B GLY* 1.3 61.6 + - - +
2420B THR* 5.8 0.2 - - - -
2421B GLN* 2.5 35.3 + - + +
2422B PHE* 3.9 7.6 - - + -
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Residues in contact with GLY2418 (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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2260B GLU* 6.1 1.3 - - - -
2262B TYR* 4.4 9.0 - - - -
2414B LEU 2.6 25.1 + - - -
2415B LEU 4.0 3.3 + - - -
2416B GLU 3.6 1.2 - - - -
2417B HIS* 1.3 76.0 - - - +
2419B LEU* 1.3 66.0 + - - -
2420B THR* 3.3 3.5 + - - -
2421B GLN 3.4 0.2 + - - -
2422B PHE* 3.0 24.3 + - - -
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Residues in contact with LEU2419 (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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2260B GLU* 5.3 5.9 + - - +
2262B TYR* 3.7 28.7 + - + +
2300B MET* 3.6 39.3 - - + +
2303B THR* 4.3 10.5 - - + -
2304B ILE* 3.7 18.4 - - + -
2307B ARG* 4.4 20.2 - - - +
2414B LEU* 3.5 23.6 - - + -
2418B GLY* 1.3 69.4 - - - -
2420B THR* 1.3 61.0 + - - +
2422B PHE* 3.3 6.3 + - - +
2423B VAL* 2.9 34.8 + - - +
2572B VAL* 3.8 14.8 - - + -
2573B LYS 5.8 0.2 - - - +
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Residues in contact with THR2420 (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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2417B HIS 5.8 0.4 - - - -
2418B GLY* 3.3 1.2 - - - -
2419B LEU* 1.3 76.8 - - - +
2421B GLN* 1.3 60.8 + - + +
2423B VAL* 3.3 3.3 + - - +
2424B GLU* 3.0 50.4 + - - +
2572B VAL* 3.6 11.5 - - - +
2573B LYS* 2.7 39.7 + - - +
2574B GLY* 5.3 2.2 - - - -
2576B PRO* 3.8 13.5 - - + -
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Residues in contact with GLN2421 (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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2397B ILE* 4.7 0.7 - - + -
2398B GLU* 2.5 46.2 + - - +
2416B GLU 4.4 0.7 - - - +
2417B HIS* 2.5 48.3 + - + +
2418B GLY 3.4 2.1 + - - +
2419B LEU 3.4 0.2 - - - -
2420B THR* 1.3 78.4 - - + +
2422B PHE* 1.3 63.7 + - - +
2424B GLU* 3.3 13.9 + - - +
2425B SER* 2.7 35.3 + - - +
2428B ARG* 6.0 0.2 - - - +
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Residues in contact with PHE2422 (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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2296B PRO* 3.8 30.7 - - + -
2300B MET* 3.2 18.8 - - + -
2397B ILE* 3.2 32.5 - - + -
2407B PHE* 4.2 2.5 - + - -
2413B ILE* 3.4 22.2 - - + -
2414B LEU* 3.4 40.4 - - + -
2417B HIS* 3.9 9.2 - - + -
2418B GLY 3.0 24.1 + - - +
2419B LEU* 3.5 4.9 - - - +
2421B GLN* 1.3 77.5 - - - +
2423B VAL* 1.3 55.8 + - - +
2425B SER* 3.8 4.5 - - - -
2426B PHE* 2.8 60.0 + + - +
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Residues in contact with VAL2423 (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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2197B MET* 4.1 13.2 - - + +
2300B MET* 3.4 18.4 - - + -
2304B ILE* 4.8 2.2 - - + -
2419B LEU* 2.9 23.9 + - - +
2420B THR 3.6 4.3 - - - +
2422B PHE* 1.3 73.9 - - - +
2424B GLU* 1.3 58.0 + - - +
2426B PHE* 4.1 0.2 - - - +
2427B THR* 2.5 40.5 + - - +
2568B ILE* 4.1 7.6 - - + -
2572B VAL* 4.1 22.4 - - + -
2576B PRO* 4.0 20.9 - - + -
2577B PHE 4.1 1.1 - - - +
2578B THR* 3.7 28.5 - - - +
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Residues in contact with GLU2424 (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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2398B GLU* 5.0 1.2 - - - +
2420B THR* 3.0 36.2 + - - +
2421B GLN* 3.8 17.8 - - - +
2423B VAL* 1.3 75.2 - - - +
2425B SER* 1.3 59.9 + - - +
2427B THR* 3.5 5.6 + - - -
2428B ARG* 3.0 56.9 + - - +
2576B PRO* 4.0 18.2 - - + +
2577B PHE 5.3 2.2 - - - +
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Residues in contact with SER2425 (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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2396B ASN 3.5 22.4 - - - +
2397B ILE* 3.6 9.5 - - - +
2398B GLU* 3.1 23.2 + - - -
2421B GLN* 2.7 23.9 + - - +
2422B PHE* 3.8 3.1 - - - -
2424B GLU* 1.3 75.4 - - - +
2426B PHE* 1.3 63.7 + - - +
2428B ARG* 3.1 18.8 + - - +
2429B GLN* 3.0 28.6 + - - +
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Residues in contact with PHE2426 (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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2195B ASN* 3.3 1.7 - - - +
2196B MET* 3.0 51.9 + - + +
2197B MET* 3.3 22.7 + - - +
2200B PHE* 3.5 39.3 - + + -
2297B GLY* 3.9 11.2 - - - -
2300B MET* 4.1 16.6 - - - -
2395B PHE* 5.0 4.0 - + + -
2397B ILE* 3.9 20.0 - - + -
2407B PHE* 3.8 21.8 - + - -
2422B PHE* 2.8 42.1 + + - +
2425B SER* 1.3 77.2 - - - +
2427B THR* 1.3 62.2 + - - +
2428B ARG 3.5 0.2 + - - -
2429B GLN* 3.6 7.6 - - - +
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Residues in contact with THR2427 (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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2195B ASN* 3.1 31.5 + - - +
2197B MET* 3.5 2.8 - - - +
2423B VAL* 2.5 26.0 + - - +
2424B GLU* 3.7 6.1 - - - -
2425B SER 3.1 0.2 - - - -
2426B PHE* 1.3 78.7 - - - +
2428B ARG* 1.3 60.6 + - + +
2577B PHE* 3.9 14.7 + - + +
2578B THR* 2.8 39.6 + - - -
2579B SER 4.1 3.8 - - - +
2581B ASN 4.7 2.5 - - - +
2582B VAL* 3.6 10.7 - - - +
2583B GLN* 4.0 15.0 + - - +
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Residues in contact with ARG2428 (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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2398B GLU* 5.4 10.7 + - - +
2421B GLN* 5.1 0.4 + - - +
2424B GLU* 3.0 54.2 + - - +
2425B SER* 3.1 17.1 + - - +
2427B THR* 1.3 79.4 - - + +
2429B GLN* 1.3 64.5 + - - +
2430B ILE 3.4 1.2 + - - -
2582B VAL* 3.3 17.2 - - - +
2583B GLN* 3.9 14.9 - - - +
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Residues in contact with GLN2429 (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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2195B ASN* 3.0 7.6 - - - +
2196B MET* 3.0 52.6 + - + +
2392B PRO* 3.5 11.3 - - - +
2394B THR 2.8 24.5 - - - +
2395B PHE* 3.8 5.1 - - - +
2396B ASN* 3.1 50.3 + - + +
2425B SER 3.0 13.7 + - - +
2426B PHE* 3.8 4.0 + - - -
2427B THR 3.6 0.6 - - - -
2428B ARG* 1.3 75.5 - - - +
2430B ILE* 1.3 71.7 + - + +
2582B VAL* 3.8 0.9 - - - -
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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