Contacts of the helix formed by residues 3154 - 3162 (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 GLY3154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3122C TYR* 3.4 32.0 - - - -
3152C TYR 3.7 1.2 + - - -
3153C ASP* 1.3 74.3 + - - +
3155C LEU* 1.3 63.8 + - - +
3156C ALA 3.4 1.1 + - - -
3157C LEU* 3.5 3.9 + - - -
3158C ALA* 3.0 26.0 + - - +
3165C VAL* 4.0 18.2 - - - +
3167C THR* 5.6 0.2 - - - -
3476C PHE* 4.8 6.3 - - - -
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Residues in contact with LEU3155 (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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3038C VAL* 3.6 32.3 - - + +
3039C SER 4.9 1.3 - - - +
3040C LEU* 4.1 26.9 - - + -
3047C VAL* 3.7 27.8 - - + -
3049C ILE* 4.3 10.1 - - + -
3122C TYR* 3.5 8.7 - - + -
3153C ASP* 2.9 23.7 + - - +
3154C GLY* 1.3 75.8 - - - +
3156C ALA* 1.3 62.8 + - - +
3158C ALA* 3.8 3.6 - - - +
3159C ALA* 3.1 20.1 + - + +
3481C LEU* 4.1 19.5 - - + -
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Residues in contact with ALA3156 (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 14.6 - - + +
3154C GLY 3.4 1.0 - - - -
3155C LEU* 1.3 76.5 - - - +
3157C LEU* 1.3 62.0 + - - +
3160C HIS* 2.8 47.0 + - + +
3476C PHE 3.8 10.8 - - - +
3477C GLY* 3.7 27.6 - - - +
3480C PHE* 4.4 3.6 - - + -
3481C LEU* 4.1 15.3 - - + +
3497C MET* 4.4 0.9 - - - -
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Residues in contact with LEU3157 (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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3136C MET* 4.3 14.4 - - + -
3154C GLY* 3.5 10.3 + - - +
3156C ALA* 1.3 77.7 - - - +
3158C ALA* 1.3 63.9 + - - +
3161C GLU* 3.0 30.3 + - + +
3163C VAL* 3.9 7.6 - - + +
3165C VAL* 4.0 21.1 - - + -
3218C PHE* 4.2 26.2 - - + -
3475C VAL* 3.7 21.3 - - + +
3476C PHE* 4.6 12.8 + - + -
3497C MET* 3.7 42.7 - - + +
3500C TRP* 5.4 4.3 - - + -
3501C ALA* 5.2 0.2 - - + -
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Residues in contact with ALA3158 (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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3047C VAL* 4.6 3.8 - - + -
3122C TYR* 3.7 23.3 - - + +
3124C PRO* 3.5 12.2 - - + +
3154C GLY 3.0 19.5 + - - +
3155C LEU 3.8 2.9 - - - +
3157C LEU* 1.3 76.0 - - - +
3159C ALA* 1.3 55.5 + - - +
3162C ASN* 2.7 36.0 + - - -
3163C VAL 3.2 24.4 + - - +
3165C VAL* 3.9 5.1 - - + +
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Residues in contact with ALA3159 (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 18.8 - - + -
3043C PHE* 3.1 34.5 - - + -
3045C GLN 5.7 0.9 - - - +
3047C VAL* 3.8 16.8 - - + +
3124C PRO* 4.2 9.8 - - - +
3155C LEU* 3.1 16.3 + - + +
3156C ALA 4.1 1.3 - - - +
3158C ALA* 1.3 80.6 - - - +
3160C HIS* 1.3 62.8 + - - +
3161C GLU 3.6 0.2 + - - -
3162C ASN* 3.9 11.3 + - - -
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Residues in contact with HIS3160 (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* 3.9 17.7 - - + +
3041C GLU 5.7 0.2 + - - -
3043C PHE* 3.5 32.9 - + - -
3156C ALA* 2.8 33.1 + - - +
3157C LEU 4.2 0.9 - - - +
3159C ALA* 1.3 76.5 - - - +
3161C GLU* 1.3 71.3 + - + +
3162C ASN* 5.9 0.2 + - - -
3480C PHE* 3.5 44.8 - + - +
3494C LYS* 4.8 10.0 - - - +
3497C MET* 3.8 25.8 - - + +
3498C LYS* 4.5 4.5 + - - -
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Residues in contact with GLU3161 (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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3157C LEU* 3.0 18.4 + - + +
3160C HIS* 1.3 83.8 - - + +
3162C ASN* 1.3 71.0 + - - +
3163C VAL* 3.4 4.6 + - + +
3494C LYS 4.6 1.2 - - - +
3497C MET* 3.4 23.6 - - + +
3498C LYS* 2.6 51.8 + - - +
3501C ALA* 3.3 23.0 - - + +
3505C ARG* 2.6 53.9 + - - -
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Residues in contact with ASN3162 (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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3043C PHE* 6.2 0.4 - - - -
3124C PRO* 3.9 16.4 + - - +
3125C ALA* 5.3 0.7 - - - -
3133C LEU* 3.6 44.1 - - + +
3134C PRO* 4.4 4.2 - - - +
3158C ALA 2.7 18.5 + - - -
3159C ALA 3.9 9.3 + - - -
3160C HIS 3.6 2.4 - - - -
3161C GLU* 1.3 77.2 - - - +
3163C VAL* 1.3 59.0 + - - +
3505C ARG* 4.7 1.9 + - - +
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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