Contacts of the helix formed by residues 3261 - 3272 (chain C) in PDB entry 2H7C
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 VAL3261 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3179C SER* 3.8 17.6 - - - +
3181C GLY* 3.5 37.9 - - - +
3257C LYS* 4.1 28.9 - - + +
3258C LYS 5.1 1.1 - - - +
3259C GLY 3.4 13.0 + - - +
3260C ASP* 1.3 74.6 + - - +
3262C LYS* 1.3 65.9 + - - +
3263C PRO* 3.4 2.5 - - - -
3264C LEU* 3.3 14.6 + - + +
3265C ALA* 3.3 17.5 + - - +
3322C VAL* 4.1 16.8 - - + -
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Residues in contact with LYS3262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3180C THR* 3.6 20.5 + - - +
3260C ASP* 3.2 19.9 + - - +
3261C VAL* 1.3 80.0 - - - +
3263C PRO* 1.3 67.2 - - + +
3265C ALA* 3.1 8.0 + - + +
3266C GLU* 2.9 43.1 + - - +
3276C THR 5.8 1.3 - - - -
3278C THR 4.5 0.6 - - - -
3279C SER* 2.6 34.6 + - - +
3282C MET* 2.9 33.3 - - + +
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Residues in contact with PRO3263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3260C ASP* 2.9 36.8 - - + +
3261C VAL 3.5 3.6 - - - -
3262C LYS* 1.3 85.5 - - + +
3264C LEU* 1.3 61.3 + - - +
3266C GLU* 3.4 9.5 + - + +
3267C GLN* 3.0 23.4 + - - +
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Residues in contact with LEU3264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3257C LYS* 3.8 13.5 - - + +
3261C VAL* 3.3 14.9 + - + +
3262C LYS 3.2 0.6 - - - -
3263C PRO* 1.3 77.1 - - - +
3265C ALA* 1.3 66.7 + - - +
3267C GLN* 3.3 10.3 + - - +
3268C ILE* 3.1 37.5 + - + +
3301C MET* 4.0 14.4 - - + -
3316C GLN* 3.3 43.3 + - + +
3319C LEU* 3.3 27.6 - - + -
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Residues in contact with ALA3265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3178C PHE* 3.8 26.2 - - + -
3179C SER 3.2 25.1 + - - +
3180C THR* 4.1 13.0 - - + -
3261C VAL 3.3 5.5 + - - +
3262C LYS* 3.1 12.9 + - + +
3264C LEU* 1.3 78.8 - - - +
3266C GLU* 1.3 62.6 + - - +
3268C ILE* 3.3 4.8 + - - +
3269C ALA* 3.0 22.7 + - - +
3282C MET* 4.2 6.2 - - - +
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Residues in contact with GLU3266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3262C LYS* 2.9 43.6 + - - +
3263C PRO* 3.7 7.4 - - + +
3265C ALA* 1.3 77.3 - - - +
3267C GLN* 1.3 56.5 + - - +
3269C ALA* 3.3 1.0 + - - +
3270C ILE* 2.9 42.8 + - + +
3276C THR* 4.0 24.8 + - + +
3282C MET* 4.0 25.8 - - + -
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Residues in contact with GLN3267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3263C PRO 3.0 16.6 + - - +
3264C LEU* 3.3 13.5 + - - +
3266C GLU* 1.3 76.2 - - - +
3268C ILE* 1.3 58.0 - - - +
3270C ILE* 3.6 8.5 + - - +
3271C THR* 2.7 36.5 + - - +
3301C MET* 3.5 27.6 - - + +
3314C GLU 5.3 5.9 + - - +
3316C GLN* 4.9 8.0 - - - +
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Residues in contact with ILE3268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3174C ILE* 4.1 23.1 - - + -
3178C PHE* 4.1 28.3 - - + -
3264C LEU* 3.1 18.1 + - + +
3265C ALA* 3.6 6.5 - - - +
3266C GLU 3.2 0.2 - - - -
3267C GLN* 1.3 75.2 - - - +
3269C ALA* 1.3 65.6 + - - +
3271C THR* 3.3 4.0 + - - -
3272C ALA* 3.0 21.7 + - - +
3286C LEU* 4.7 10.1 - - + -
3297C THR* 3.9 7.1 - - + +
3301C MET* 3.8 25.8 - - + -
3303C PHE* 4.7 1.3 - - + -
3319C LEU* 3.6 41.7 - - + -
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Residues in contact with ALA3269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3265C ALA 3.0 16.8 + - - +
3266C GLU 3.3 4.7 + - - +
3268C ILE* 1.3 77.4 - - - +
3270C ILE* 1.3 57.3 + - - +
3272C ALA* 3.1 5.5 + - - -
3273C GLY 3.0 5.0 + - - -
3274C CYS* 2.7 48.3 + - + +
3276C THR* 4.1 5.6 - - + -
3282C MET* 3.9 27.8 - - + -
3286C LEU* 4.5 11.4 - - + +
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Residues in contact with ILE3270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3266C GLU* 2.9 30.5 + - + +
3267C GLN* 3.9 7.6 - - - +
3269C ALA* 1.3 74.1 - - - +
3271C THR* 1.3 60.5 + - - +
3273C GLY* 2.8 20.3 + - - -
3274C CYS 3.8 9.0 - - - +
3276C THR* 3.8 19.5 - - + +
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Residues in contact with THR3271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3267C GLN* 2.7 26.8 + - - +
3268C ILE 3.3 4.7 + - - -
3270C ILE* 1.3 77.7 - - - +
3272C ALA* 1.3 60.5 + - - +
3273C GLY 3.3 0.7 + - - -
3297C THR* 3.9 19.5 + - + +
3300C LYS* 3.8 48.6 + - + -
3301C MET* 3.7 14.9 - - - -
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Residues in contact with ALA3272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3268C ILE 3.0 16.8 + - - +
3269C ALA 3.1 5.3 + - - +
3271C THR* 1.3 75.8 - - - +
3273C GLY* 1.3 58.1 + - - +
3274C CYS* 3.4 3.4 - - - -
3286C LEU* 3.8 24.7 - - + -
3289C LYS* 3.0 32.7 + - + +
3293C GLU 5.6 0.2 - - - +
3294C LEU* 4.8 2.0 - - + -
3297C THR* 3.5 22.2 + - + +
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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