Contacts of the helix formed by residues 2195 - 2207 (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 ASN2195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2193B GLY 4.3 0.2 - - - +
2194B SER* 1.3 76.0 - - - +
2196B MET* 1.3 69.3 + - - +
2197B MET* 3.0 4.4 + - - +
2198B PHE* 2.9 21.4 + - - +
2199B ALA* 3.1 21.8 + - - +
2426B PHE 3.3 9.2 - - - +
2427B THR* 3.1 23.2 + - - +
2429B GLN 3.0 16.8 - - - +
2431B ALA* 3.9 2.3 - - - +
2579B SER 2.8 22.8 + - - -
2580B PHE 3.1 10.2 + - - +
2581B ASN 3.3 13.3 + - - -
2582B VAL* 3.5 13.5 - - + -
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Residues in contact with MET2196 (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* 1.3 75.3 - - - +
2197B MET* 1.3 65.5 + - - +
2198B PHE 3.2 0.9 - - - -
2199B ALA* 3.7 12.6 - - + -
2200B PHE* 3.1 34.1 + - + +
2390B LEU 3.9 8.5 - - - +
2391B LEU* 5.2 0.4 - - - -
2392B PRO* 3.6 27.1 - - + -
2395B PHE* 4.4 9.0 - - + -
2426B PHE* 3.0 36.3 + - + +
2429B GLN* 3.0 34.9 + - + +
2430B ILE 3.6 7.0 - - - +
2431B ALA* 3.4 40.2 - - + -
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Residues in contact with MET2197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2195B ASN* 3.0 9.5 + - - +
2196B MET* 1.3 76.7 - - - +
2198B PHE* 1.3 58.1 + - - +
2201B PHE* 3.1 18.0 + - - +
2300B MET* 4.2 16.6 - - + +
2301B TYR* 2.7 41.1 + - + +
2304B ILE* 5.3 0.2 - - + -
2423B VAL* 4.1 13.5 - - + -
2426B PHE* 3.3 21.0 + - - -
2427B THR* 3.5 29.2 - - - +
2564B ILE* 5.3 2.5 - - + -
2568B ILE* 4.0 29.2 - - + -
2578B THR* 3.5 19.7 - - + +
2579B SER 3.8 9.9 - - - +
2580B PHE* 4.1 6.1 - - + -
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Residues in contact with PHE2198 (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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2194B SER* 4.1 13.5 - - - -
2195B ASN* 2.9 13.0 + - - +
2197B MET* 1.3 76.2 - - - +
2199B ALA* 1.3 71.6 + - - +
2201B PHE* 3.2 1.7 + - - +
2202B ALA* 2.9 23.7 + - + +
2348B TYR* 3.4 39.0 - + - -
2351B HIS* 3.8 18.6 - + - -
2352B LEU* 3.2 44.2 - - + -
2387B TRP* 4.1 8.1 - + - -
2390B LEU* 4.0 26.0 - - + -
2517B ILE* 5.4 0.7 - - + -
2580B PHE* 3.5 36.1 - + + +
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Residues in contact with ALA2199 (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 16.7 + - - +
2196B MET* 4.0 25.8 - - + +
2197B MET 3.5 0.2 - - - -
2198B PHE* 1.3 84.3 - - - +
2200B PHE* 1.3 63.2 + - + +
2202B ALA* 3.5 4.0 + - - +
2203B GLN* 3.2 20.1 + - - +
2390B LEU* 4.2 23.8 - - + +
2391B LEU* 5.1 4.3 - - + -
2431B ALA* 4.8 1.3 - - + -
2704B BOG 3.9 13.4 - - + +
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Residues in contact with PHE2200 (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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2196B MET* 3.1 35.5 + - + +
2199B ALA* 1.3 78.5 - - + +
2201B PHE* 1.3 61.3 + - - +
2203B GLN* 3.3 6.5 + - + +
2204B HIS* 2.8 31.4 + - - +
2295B VAL* 3.5 25.8 - - + -
2297B GLY* 3.7 18.2 - - - +
2298B LEU* 3.8 12.3 - - + +
2301B TYR* 3.6 17.7 - - + -
2391B LEU* 5.2 7.4 - - + -
2395B PHE* 4.2 21.1 - + - -
2407B PHE* 3.9 21.8 - + - -
2408B LEU* 6.3 0.7 - - + -
2426B PHE* 3.5 33.0 - + + -
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Residues in contact with PHE2201 (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 3.1 20.4 + - - +
2198B PHE 3.2 4.5 + - - +
2200B PHE* 1.3 74.2 - - - +
2202B ALA* 1.3 57.8 + - - +
2204B HIS* 4.4 4.0 - - - -
2205B PHE* 2.8 59.4 + + + +
2301B TYR* 3.4 30.3 - + - +
2305B TRP* 4.5 24.5 - + - -
2340B THR* 5.1 2.2 - - + -
2343B ILE* 4.0 21.1 - - + -
2344B VAL* 3.8 22.4 - - + -
2348B TYR* 3.6 25.6 - + + -
2564B ILE* 4.0 15.3 - - + -
2567B LEU* 5.1 0.2 - - + -
2580B PHE* 3.8 17.5 - + + -
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Residues in contact with ALA2202 (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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2198B PHE* 2.9 25.8 + - + +
2199B ALA* 3.5 6.7 - - - +
2200B PHE 3.2 0.2 - - - -
2201B PHE* 1.3 78.2 - - - +
2203B GLN* 1.3 53.7 + - - +
2205B PHE* 4.7 1.1 - - - -
2206B THR* 2.7 39.4 + - - +
2348B TYR* 3.0 31.4 - - + +
2385B TYR* 4.5 7.4 - - + -
2387B TRP* 4.7 5.8 - - + -
2390B LEU* 4.9 3.6 - - + -
2704B BOG 4.9 6.9 - - + +
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Residues in contact with GLN2203 (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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2199B ALA 3.2 11.2 + - - +
2200B PHE* 3.6 12.6 - - + +
2201B PHE 3.2 0.4 - - - -
2202B ALA* 1.3 78.1 - - - +
2204B HIS* 1.3 64.2 + - - +
2206B THR* 3.6 4.5 + - - -
2207B ALA* 3.2 24.9 + - + +
2295B VAL* 5.9 1.8 - - - +
2298B LEU* 3.4 34.0 - - + +
2388B HIS* 5.6 1.6 - - - -
2704B BOG 2.9 49.2 + - + +
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Residues in contact with HIS2204 (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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2200B PHE 2.8 17.7 + - - +
2201B PHE* 3.9 5.0 - - - +
2203B GLN* 1.3 75.1 - - - +
2205B PHE* 1.3 70.3 + - - +
2207B ALA* 3.2 12.0 + - - +
2232B HIS* 3.2 43.5 + + - -
2233B ILE* 4.9 5.2 - - + +
2292B PHE* 3.4 32.7 - + - -
2298B LEU* 3.9 17.9 - - + +
2301B TYR* 3.6 26.1 - - + +
2302B ALA* 3.8 15.0 + - - -
2305B TRP* 3.4 33.5 + + - -
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Residues in contact with PHE2205 (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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2201B PHE* 2.8 40.2 + + + +
2202B ALA 4.2 0.7 - - - +
2204B HIS* 1.3 80.7 + - - +
2206B THR* 1.3 75.6 + - + +
2207B ALA 3.0 4.9 + - - -
2208B GLN* 2.7 51.0 + - - +
2209B PHE* 3.7 21.5 - + - -
2228B VAL* 3.8 18.2 - - + -
2232B HIS* 4.4 1.3 - - - -
2340B THR* 3.6 28.7 - - + -
2344B VAL* 3.7 22.4 - - + -
2348B TYR* 5.0 4.0 - + - -
2385B TYR* 4.6 2.0 - - - -
2534B LEU* 4.1 9.0 - - + -
2701B ACD 3.6 25.1 - - - -
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Residues in contact with THR2206 (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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2202B ALA 2.7 23.4 + - - +
2203B GLN* 3.6 5.4 + - - -
2205B PHE* 1.3 83.2 - - + +
2207B ALA* 1.3 58.7 + - - +
2208B GLN 3.1 1.2 + - - -
2209B PHE* 3.2 16.7 + - + -
2210B PHE* 2.9 50.3 + - + +
2385B TYR* 3.4 42.7 - - + +
2704B BOG 4.7 11.4 + - - +
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Residues in contact with ALA2207 (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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2203B GLN* 3.2 21.0 + - + +
2204B HIS 3.2 10.3 + - - +
2205B PHE 3.0 1.4 + - - -
2206B THR* 1.3 77.2 - - - +
2208B GLN* 1.3 56.6 + - - +
2209B PHE 3.3 0.2 - - - -
2210B PHE 4.0 6.9 - - - +
2211B LYS* 3.0 25.1 - - - +
2232B HIS* 4.7 1.3 - - - -
2289B GLN* 3.1 15.1 + - - +
2291B VAL* 5.6 0.9 - - + -
2292B PHE* 3.4 28.0 - - + -
2704B BOG 5.1 7.4 - - - +
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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