Contacts of the helix formed by residues 3221 - 3233 (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 SER3221 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C COA 3.4 26.2 + - - +
3141C GLY* 4.4 3.6 - - - -
3142C GLY 4.7 0.2 - - - -
3220C GLU* 1.3 86.4 - - - +
3222C ALA* 1.3 64.2 + - - -
3224C GLY* 2.8 16.7 + - - +
3225C GLU* 2.9 13.9 + - - +
3246C GLU 2.8 12.3 + - - -
3247C SER 3.1 15.6 + - - -
3248C GLY* 3.7 5.6 - - - -
3255C LEU* 4.6 4.0 - - - -
3426C PHE* 4.9 2.6 - - - -
3468C HIS* 2.7 26.5 + - - -
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Residues in contact with ALA3222 (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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3C COA 4.9 0.2 - - - -
3140C HIS 4.5 0.9 - - - -
3141C GLY* 4.0 1.7 - - - -
3142C GLY 3.9 5.8 - - - +
3143C GLY* 3.4 30.7 - - - +
3144C LEU* 3.5 28.8 - - + +
3170C TYR* 4.6 1.1 - - - +
3220C GLU 3.2 0.4 + - - -
3221C SER* 1.3 81.6 + - - +
3223C GLY* 1.3 57.8 + - - +
3225C GLU* 3.4 4.0 + - - +
3226C SER* 2.9 31.5 + - - -
3255C LEU* 3.8 15.8 - - + +
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Residues in contact with GLY3223 (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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3139C ILE* 3.2 33.4 - - - +
3140C HIS 3.6 7.0 - - - -
3141C GLY* 3.7 3.4 - - - -
3219C GLY* 3.7 7.6 - - - -
3220C GLU 2.9 8.5 + - - -
3222C ALA* 1.3 77.3 - - - +
3224C GLY* 1.3 63.8 + - - +
3226C SER* 3.4 3.0 + - - -
3227C VAL* 3.1 27.0 + - - +
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Residues in contact with GLY3224 (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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3219C GLY* 3.3 18.2 - - - -
3220C GLU* 3.4 9.4 - - - -
3221C SER 2.8 8.6 + - - -
3223C GLY* 1.3 76.4 - - - +
3225C GLU* 1.3 61.8 + - - +
3227C VAL* 3.3 1.9 + - - -
3228C SER* 3.1 10.0 + - - -
3245C SER* 2.9 27.4 + - - -
3246C GLU 4.2 0.7 - - - -
3248C GLY 3.0 15.7 - - - +
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Residues in contact with GLU3225 (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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3144C LEU* 4.1 6.2 - - - +
3191C HIS* 3.7 11.4 - - - -
3221C SER 2.9 5.9 + - - +
3222C ALA 3.6 7.3 - - - +
3223C GLY 3.3 0.2 - - - -
3224C GLY* 1.3 76.8 - - - +
3226C SER* 1.3 59.2 + - - +
3228C SER* 3.2 3.3 + - - -
3229C VAL* 2.9 38.6 + - - +
3248C GLY 3.3 1.2 + - - -
3249C VAL 3.3 32.8 - - - +
3250C ALA* 4.1 3.8 - - - -
3255C LEU* 3.3 40.9 - - + +
3256C VAL* 3.5 18.9 - - + +
3321C THR* 2.7 29.0 + - - -
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Residues in contact with SER3226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3139C ILE* 4.0 8.4 - - - +
3144C LEU* 4.0 5.2 - - - +
3170C TYR* 4.9 0.2 + - - -
3191C HIS* 3.3 18.5 - - - -
3194C GLN* 3.0 37.6 + - - -
3222C ALA 2.9 20.0 + - - -
3223C GLY 3.5 6.3 - - - -
3224C GLY 3.2 0.2 - - - -
3225C GLU* 1.3 79.6 + - - +
3227C VAL* 1.3 64.8 + - - +
3229C VAL* 3.1 3.2 + - - +
3230C LEU* 2.9 29.7 + - - +
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Residues in contact with VAL3227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3139C ILE* 3.9 13.9 - - + -
3217C ILE* 3.8 15.0 - - + +
3218C PHE* 3.9 23.1 - - - +
3223C GLY 3.1 18.2 + - - +
3224C GLY 3.3 7.8 + - - +
3226C SER* 1.3 75.6 - - - +
3228C SER* 1.3 63.9 + - - +
3230C LEU* 3.2 5.0 + - - +
3231C VAL* 3.0 21.7 + - - +
3243C ALA* 3.7 29.8 - - + -
3244C ILE 3.8 19.5 - - - +
3245C SER* 3.5 12.6 - - - +
3346C TYR* 4.1 2.9 - - + -
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Residues in contact with SER3228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3224C GLY 3.1 10.9 + - - -
3225C GLU 3.4 4.7 - - - -
3227C VAL* 1.3 78.3 - - - +
3229C VAL* 1.3 61.1 + - - +
3231C VAL* 3.3 5.7 + - - +
3232C LEU* 3.3 25.5 + - - +
3249C VAL* 3.7 8.0 - - - +
3250C ALA* 2.9 37.7 + - - +
3346C TYR* 3.3 24.5 + - - -
3433C VAL* 4.4 9.2 - - - +
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Residues in contact with VAL3229 (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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3191C HIS* 4.5 9.2 - - + +
3225C GLU* 2.9 41.2 + - - +
3226C SER* 3.1 9.8 + - - +
3228C SER* 1.3 76.8 - - - +
3230C LEU* 1.3 57.5 + - + +
3232C LEU* 3.0 13.3 + - + +
3233C SER* 3.0 23.7 + - - -
3250C ALA* 4.3 11.4 - - + -
3256C VAL* 5.5 1.3 - - + -
3321C THR* 4.3 11.0 - - + +
3327C LEU* 3.6 35.9 - - + -
3328C LEU* 4.2 15.6 - - + +
3332C PRO* 6.0 0.4 - - + -
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Residues in contact with LEU3230 (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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3139C ILE* 3.9 25.8 - - + -
3191C HIS* 4.6 7.2 - - + +
3194C GLN* 4.4 14.8 - - + +
3195C VAL* 3.7 31.2 - - + +
3198C LEU* 4.2 15.3 - - + -
3217C ILE* 4.0 19.7 - - + -
3226C SER 2.9 19.1 + - - +
3227C VAL 3.6 5.6 - - - +
3229C VAL* 1.3 74.3 - - + +
3231C VAL* 1.3 64.7 + - - +
3233C SER* 3.2 21.9 + - - +
3236C ALA* 4.1 9.2 - - + +
3240C PHE* 3.8 16.7 - - + -
3327C LEU* 4.7 10.5 - - + -
3342C HIS* 3.8 1.9 + - - -
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Residues in contact with VAL3231 (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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3227C VAL* 3.0 22.0 + - + +
3228C SER* 3.4 12.3 - - - +
3230C LEU* 1.3 76.7 - - - +
3232C LEU* 1.3 62.3 + - + +
3233C SER 4.9 0.5 - - - +
3240C PHE* 4.0 9.9 - - + -
3243C ALA* 3.9 26.5 - - + -
3341C PHE* 3.3 17.7 - - + +
3342C HIS* 3.2 39.6 + - + +
3344C VAL* 5.0 2.5 - - + -
3346C TYR* 4.4 12.6 - - + -
3437C HIS* 4.2 19.5 - - + +
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Residues in contact with LEU3232 (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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3228C SER* 3.4 17.5 - - - +
3229C VAL* 3.0 11.2 + - + +
3231C VAL* 1.3 82.7 - - + +
3233C SER* 1.3 57.9 + - - +
3234C PRO* 4.0 5.4 - - - +
3250C ALA* 3.8 14.4 - - + -
3327C LEU 4.8 0.2 - - - +
3328C LEU* 4.2 6.3 - - + +
3332C PRO* 3.8 33.7 - - + -
3335C LEU* 3.7 38.3 - - + +
3336C GLN* 4.3 14.6 - - + -
3340C ASN 4.2 8.6 - - - +
3341C PHE* 3.9 33.0 - - + -
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Residues in contact with SER3233 (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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3229C VAL 3.0 11.9 + - - -
3230C LEU* 3.2 18.5 + - - +
3231C VAL 4.9 0.9 - - - +
3232C LEU* 1.3 78.3 - - - +
3234C PRO* 1.3 66.5 - - - +
3235C LEU* 3.3 14.6 + - - +
3236C ALA 3.3 11.3 + - - -
3237C LYS* 3.8 6.1 + - - +
3327C LEU* 2.8 47.6 + - - +
3328C LEU* 4.8 0.7 - - - -
3342C HIS* 5.1 2.1 + - - -
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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