Contacts of the helix formed by residues 2428 - 2433 (chain B) in PDB entry 1I4E
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 SER2428 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2424B SER* 2.6 28.9 + - - -
2426B CYS 2.8 0.8 - - - -
2427B GLN* 1.3 86.9 + - - +
2429B LEU* 1.3 57.3 + - - +
2431B GLU* 3.9 4.5 - - - +
2432B ARG* 3.1 31.7 + - - +
2442B ILE* 3.8 8.4 - - - +
2445B GLU* 2.9 32.6 + - - +
2446B VAL* 4.0 16.5 - - - +
2449B GLU* 4.6 4.3 - - - +
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Residues in contact with LEU2429 (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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2273B THR* 4.3 8.3 - - + -
2274B PHE* 3.8 32.1 - - + -
2277B LEU* 4.5 2.5 - - + -
2356B PHE* 5.1 1.6 - - + -
2425B LEU* 2.7 39.3 + - + +
2426B CYS* 2.9 3.5 + - - +
2428B SER* 1.3 76.4 - - - +
2430B ARG* 1.3 58.8 + - - +
2431B GLU 2.8 10.5 + - - -
2432B ARG 3.2 0.2 + - - -
2433B CYS* 3.0 60.1 + - - +
2439B ILE* 3.6 18.6 - - + -
2442B ILE* 3.4 27.6 - - + +
2476B PHE* 4.0 3.1 - - + -
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Residues in contact with ARG2430 (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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254A TRP* 5.7 1.0 - - - +
255A GLY* 3.4 34.6 - - - +
2272B THR* 6.4 1.8 - - - -
2273B THR* 4.1 23.9 - - + +
2277B LEU* 6.1 3.1 - - - -
2423B GLN* 5.7 3.0 + - - -
2426B CYS* 2.6 32.2 + - - +
2427B GLN* 4.1 29.3 + - - +
2429B LEU* 1.3 73.0 - - - +
2431B GLU* 1.3 60.0 + - + +
2433B CYS* 5.1 2.2 - - - -
2434B PRO* 3.9 12.9 - - - +
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Residues in contact with GLU2431 (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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2427B GLN 3.5 19.7 - - - +
2428B SER* 3.8 3.3 + - - +
2429B LEU 2.8 3.0 + - - -
2430B ARG* 1.3 82.4 - - + +
2432B ARG* 1.3 80.1 + - - +
2434B PRO* 2.8 25.9 - - - +
2435B ARG* 3.2 29.1 + - - -
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Residues in contact with ARG2432 (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 SER 3.1 16.3 + - - +
2431B GLU* 1.3 89.4 + - - +
2433B CYS* 1.3 62.9 + - - +
2434B PRO 3.4 1.1 - - - -
2435B ARG* 3.8 25.8 + - - +
2436B GLY 3.7 3.5 + - - -
2437B ASP* 3.0 51.3 + - - +
2441B THR* 4.1 15.9 + - - +
2442B ILE* 3.9 33.4 - - + +
2445B GLU* 2.5 34.7 + - - +
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Residues in contact with CYS2433 (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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2277B LEU* 3.9 26.7 - - + -
2429B LEU* 3.0 44.5 + - - +
2430B ARG* 5.0 1.8 - - - -
2432B ARG* 1.3 74.6 - - - +
2434B PRO* 1.3 74.6 - - + +
2435B ARG 3.3 0.2 - - - -
2436B GLY* 3.2 10.6 + - - +
2437B ASP 4.9 5.2 - - - +
2439B ILE* 5.2 0.2 - - - -
2442B ILE* 4.4 5.2 - - - -
2475B VAL* 6.4 0.9 - - - -
2476B PHE* 3.8 34.5 - - - +
2477B PRO* 4.6 7.8 - - - +
2478B SER* 5.4 3.2 + - - +
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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