Contacts of the helix formed by residues 3477 - 3481 (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 GLY3477 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3103C ASN* 4.8 0.2 - - - -
3156C ALA* 3.7 7.1 - - - +
3473C PHE 3.4 0.2 + - - -
3474C SER 3.3 4.8 + - - -
3475C VAL 3.3 5.5 + - - -
3476C PHE* 1.3 77.6 - - - +
3478C ALA* 1.3 65.6 + - - +
3479C PRO* 3.1 3.6 - - - -
3480C PHE* 2.9 25.4 + - - +
3481C LEU* 3.6 4.2 + - - +
3493C SER* 3.2 20.2 - - - -
3497C MET* 3.8 12.7 - - - -
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Residues in contact with ALA3478 (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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3103C ASN* 3.5 35.7 - - + +
3455C PHE* 3.7 17.5 - - + -
3473C PHE* 2.9 28.5 + - + +
3476C PHE 3.3 2.8 + - - -
3477C GLY* 1.3 73.0 - - - +
3479C PRO* 1.3 65.3 - - + +
3481C LEU* 2.9 1.4 + - - -
3482C LYS* 2.7 36.1 + - + +
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Residues in contact with PRO3479 (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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3455C PHE* 4.0 13.7 - - + -
3473C PHE* 3.3 13.7 - - + +
3474C SER* 6.1 0.2 - - - +
3477C GLY* 3.2 6.5 - - - -
3478C ALA* 1.3 91.6 - - + +
3480C PHE* 1.3 66.3 + - + +
3482C LYS 3.6 11.6 - - - +
3485C ALA* 3.7 26.8 - - + +
3489C GLU* 3.8 24.9 - - + +
3490C ILE* 3.8 25.0 - - + +
3493C SER* 3.9 6.7 - - - +
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Residues in contact with PHE3480 (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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3040C LEU* 3.8 17.0 - - + +
3156C ALA* 4.4 7.6 - - + -
3160C HIS* 3.5 31.0 - + - +
3477C GLY* 2.9 16.8 + - - +
3479C PRO* 1.3 81.9 - - + +
3481C LEU* 1.3 67.0 + - - +
3482C LYS 4.6 0.9 - - - -
3490C ILE* 3.8 21.1 - - + -
3493C SER* 3.8 15.0 - - - -
3494C LYS* 3.4 42.6 - - + -
3497C MET* 3.4 28.3 - - + -
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Residues in contact with LEU3481 (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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3040C LEU* 4.2 9.2 - - + -
3103C ASN* 3.4 43.3 - - - +
3104C ARG* 4.4 5.8 - - - -
3105C LYS* 3.8 18.6 + - - +
3153C ASP* 3.8 26.7 - - + +
3155C LEU* 4.1 26.0 - - + -
3156C ALA* 4.1 18.4 - - + +
3476C PHE 4.4 0.4 - - - +
3477C GLY 3.9 6.1 - - - +
3478C ALA 2.9 1.7 + - - +
3480C PHE* 1.3 90.0 - - - +
3482C LYS* 1.3 63.7 + - - +
3483C GLU 4.1 0.2 + - - -
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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