Contacts of the helix formed by residues 2387 - 2391 (chain B) in PDB entry 1DCX
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 TRP2387 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2701 ACD 3.1 42.4 - - + -
2704 BOG 3.6 13.9 - - + +
2198B PHE* 4.1 6.7 - + - -
2202B ALA* 4.7 2.5 - - + -
2348B TYR* 3.7 12.6 - - - -
2352B LEU* 3.9 20.9 - - + -
2384B LEU 2.8 30.3 + - - -
2385B TYR* 2.7 41.2 + + - +
2386B HIS* 1.3 69.9 - - - +
2388B HIS* 1.3 62.8 + - - +
2389B PRO* 3.1 8.3 - - - -
2390B LEU* 3.1 45.1 + - + +
2434B VAL* 4.2 10.5 - - + -
2508B LEU* 5.6 0.2 - - + -
2518B PHE* 3.4 30.3 - + - -
2522B MET* 3.1 21.7 - - + +
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Residues in contact with HIS2388 (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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2704 BOG 4.3 35.6 - - + +
2203B GLN* 5.6 1.3 - - - -
2386B HIS* 3.2 34.7 + - + +
2387B TRP* 1.3 66.9 - - - +
2389B PRO* 1.3 59.0 - - + +
2390B LEU 2.7 16.8 + - - -
2391B LEU* 2.8 28.9 + - + +
2440B VAL* 4.7 6.1 - - + -
2441B PRO* 3.6 6.5 - - - +
2444B VAL* 3.9 27.5 - - + +
2447B VAL* 3.2 34.5 - - + +
2448B ALA* 5.1 2.9 - - - -
2451B SER* 5.0 0.2 - - - -
2504B TYR* 4.2 9.9 - - - +
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Residues in contact with PRO2389 (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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2184B ARG* 2.8 21.7 + - - -
2387B TRP* 3.1 9.4 - - - -
2388B HIS* 1.3 92.5 - - + +
2390B LEU* 1.3 56.6 + - - +
2391B LEU 3.2 0.4 - - - -
2432B GLY* 3.2 12.3 - - - -
2433B ARG 3.2 23.1 - - - +
2434B VAL* 3.9 17.3 - - + +
2439B ASN* 3.1 25.6 - - + +
2440B VAL* 3.8 19.1 - - + -
2441B PRO* 4.0 1.5 - - + -
2508B LEU* 3.9 20.9 - - + -
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Residues in contact with LEU2390 (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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2704 BOG 3.8 17.9 - - + -
2194B SER* 4.4 1.1 - - - -
2196B MET* 3.9 2.2 - - - +
2198B PHE* 4.0 28.9 - - + -
2199B ALA* 4.2 13.0 - - + -
2202B ALA* 4.9 2.5 - - + -
2387B TRP* 3.1 36.0 + - + +
2388B HIS 2.7 1.4 + - - -
2389B PRO* 1.3 79.9 - - - +
2391B LEU* 1.3 60.7 + - - +
2392B PRO* 3.5 2.6 - - - +
2431B ALA* 3.4 29.7 - - + +
2432B GLY 2.9 35.4 + - - +
2434B VAL* 3.9 10.0 - - + +
2517B ILE* 3.9 19.7 - - + -
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Residues in contact with LEU2391 (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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2704 BOG 3.8 23.8 - - + -
2184B ARG* 2.8 32.8 + - - -
2187B PHE* 4.7 0.2 - - - -
2196B MET* 5.2 0.7 - - - -
2199B ALA* 5.1 7.9 - - + -
2200B PHE* 5.2 8.1 - - + -
2388B HIS* 2.8 22.1 + - - +
2390B LEU* 1.3 77.5 - - - +
2392B PRO* 1.3 74.3 - - + +
2395B PHE* 4.1 14.8 - - + -
2404B PHE* 3.6 33.0 - - + -
2441B PRO* 3.3 4.8 - - + +
2444B VAL* 4.9 13.5 - - + -
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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