Contacts of the helix formed by residues 3426 - 3439 (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 PHE3426 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C COA 4.6 7.0 - - + -
3221C SER* 4.9 2.9 - - - -
3247C SER* 3.5 33.4 - - - -
3248C GLY* 4.2 5.4 - - - +
3252C THR* 4.5 10.5 - - + -
3350C ILE* 4.3 6.1 - - + -
3354C GLU* 3.4 41.1 - - + +
3355C PHE* 5.1 1.1 - + - -
3359C ILE* 3.7 31.4 - - + -
3422C ALA* 2.8 18.1 + - - +
3424C VAL 3.6 0.6 - - - -
3425C MET* 1.3 112.6 - - + +
3427C GLY* 1.3 63.9 + - - +
3428C VAL 3.5 1.3 - - - -
3429C PRO* 3.6 2.4 - - - +
3430C SER* 2.8 33.1 + - - +
3468C HIS* 3.9 9.6 - + - -
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Residues in contact with GLY3427 (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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3350C ILE* 4.0 24.5 - - - +
3354C GLU* 5.5 0.8 - - - +
3422C ALA 3.1 10.0 + - - -
3423C ASP* 3.8 7.0 - - - -
3426C PHE* 1.3 78.9 - - - +
3428C VAL* 1.3 62.6 + - - +
3430C SER* 3.7 1.7 - - - -
3431C VAL* 3.2 27.5 + - - +
3540C LYS* 4.4 14.4 - - - -
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Residues in contact with VAL3428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3423C ASP* 2.8 26.8 + - + +
3424C VAL* 5.0 1.8 - - - -
3427C GLY* 1.3 69.2 - - - -
3429C PRO* 1.3 69.6 - - + +
3430C SER 3.3 0.2 + - - -
3431C VAL* 3.3 1.4 + - - +
3432C ILE* 3.0 50.7 + - + +
3540C LYS* 5.3 0.4 - - + -
3543C GLU* 3.9 22.9 - - + -
3544C VAL* 3.9 20.0 - - + +
3547C TRP* 3.6 37.7 - - + -
3548C THR* 5.2 0.4 - - - +
3551C PHE* 6.3 1.3 - - + -
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Residues in contact with PRO3429 (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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3249C VAL* 3.7 12.8 - - + -
3251C LEU* 3.7 38.8 - - + +
3252C THR* 4.1 0.9 - - - +
3423C ASP 3.4 2.5 - - - +
3424C VAL 3.2 26.7 - - - +
3425C MET 3.7 10.5 - - - +
3426C PHE 3.5 9.9 - - - +
3428C VAL* 1.3 98.4 - - + +
3430C SER* 1.3 56.6 + - - +
3432C ILE* 3.4 6.7 + - + +
3433C VAL* 3.0 33.6 + - - +
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Residues in contact with SER3430 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3248C GLY 4.6 6.1 + - - -
3249C VAL* 3.8 20.4 - - - +
3348C VAL* 3.8 19.8 - - - +
3349C GLY 4.5 1.6 + - - -
3350C ILE* 3.5 24.4 - - - +
3426C PHE* 2.8 24.3 + - - -
3427C GLY 3.7 1.8 - - - -
3429C PRO* 1.3 77.4 - - - +
3431C VAL* 1.3 57.9 + - - +
3433C VAL* 3.4 3.1 + - - +
3434C ALA* 2.9 28.4 + - - +
3446C MET* 3.9 5.6 - - - -
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Residues in contact with VAL3431 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3350C ILE* 6.0 0.2 - - + -
3427C GLY 3.2 17.2 + - - +
3430C SER* 1.3 75.9 - - - +
3432C ILE* 1.3 58.2 + - - +
3434C ALA* 3.2 1.8 + - - +
3435C ARG* 2.8 48.8 + - - +
3446C MET* 3.8 21.5 - - + -
3520C TYR* 3.3 21.1 - - - +
3539C LEU* 3.4 33.7 - - + +
3540C LYS* 4.0 9.2 - - + -
3544C VAL* 4.0 13.9 - - + -
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Residues in contact with ILE3432 (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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3251C LEU* 3.4 21.5 - - + -
3336C GLN* 4.8 0.7 - - - +
3428C VAL* 3.0 41.1 + - + +
3429C PRO* 3.6 7.4 - - + +
3431C VAL* 1.3 77.8 - - - +
3433C VAL* 1.3 60.6 + - - +
3435C ARG* 3.4 7.6 + - - +
3436C ASN* 3.1 43.5 + - - +
3544C VAL* 4.0 17.3 - - + -
3548C THR* 4.3 14.8 - - - +
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Residues in contact with VAL3433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3228C SER* 4.4 11.9 - - - +
3249C VAL* 3.9 21.8 - - + -
3250C ALA* 5.5 1.8 - - + -
3251C LEU* 3.7 20.0 - - + +
3336C GLN* 3.4 23.5 + - - +
3346C TYR* 3.8 29.4 - - + +
3348C VAL* 4.8 1.6 - - + -
3429C PRO 3.0 20.7 + - - +
3430C SER 3.8 4.5 - - - +
3432C ILE* 1.3 74.7 - - - +
3434C ALA* 1.3 57.8 + - - +
3436C ASN* 3.4 1.9 + - - +
3437C HIS* 3.0 28.1 + - + +
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Residues in contact with ALA3434 (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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3348C VAL* 4.5 8.7 - - + -
3430C SER 2.9 17.7 + - - +
3431C VAL 3.5 2.7 - - - +
3433C VAL* 1.3 79.1 - - - +
3435C ARG* 1.3 57.3 + - - +
3437C HIS* 3.4 1.9 + - - -
3438C ARG* 2.9 29.5 + - - +
3444C THR* 3.7 17.0 - - + +
3446C MET* 3.5 35.9 - - + -
3520C TYR* 3.9 7.0 - - + -
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Residues in contact with ARG3435 (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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3431C VAL* 2.8 31.6 + - - +
3432C ILE* 3.8 7.6 - - - +
3434C ALA* 1.3 77.0 - - - +
3436C ASN* 1.3 57.9 + - - +
3438C ARG* 3.3 23.0 + - - +
3439C ASP* 2.9 38.4 + - - +
3520C TYR* 3.5 19.3 + - + +
3524C GLU* 2.8 33.1 + - - +
3541C ASP* 3.0 35.2 + - - +
3544C VAL* 3.5 27.4 - - - +
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Residues in contact with ASN3436 (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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3336C GLN* 3.6 45.6 + - + +
3337C ALA* 4.4 1.2 + - - -
3339C ARG* 3.0 30.4 + - - +
3341C PHE* 3.7 6.6 - - + -
3432C ILE* 3.1 34.4 + - - +
3433C VAL 3.8 0.4 - - - +
3435C ARG* 1.3 76.7 - - - +
3437C HIS* 1.3 67.1 + - - +
3439C ASP* 3.4 8.3 + - - +
3440C ALA* 3.2 21.3 + - - +
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Residues in contact with HIS3437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3231C VAL* 4.2 11.3 - - + +
3341C PHE* 3.7 20.1 - + - -
3342C HIS 3.9 19.5 - - - -
3344C VAL* 2.6 29.7 + - + -
3346C TYR* 3.3 38.7 - + + +
3433C VAL* 3.0 19.4 + - + +
3434C ALA* 3.7 6.1 - - - +
3436C ASN* 1.3 75.4 - - - +
3438C ARG* 1.3 63.9 + - - +
3440C ALA* 3.1 16.5 + - - +
3442C ALA* 3.2 33.0 + - + +
3443C PRO 3.8 2.2 - - - -
3444C THR* 3.3 19.3 - - + +
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Residues in contact with ARG3438 (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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3434C ALA 2.9 16.7 + - - +
3435C ARG* 3.5 23.8 + - - +
3437C HIS* 1.3 78.5 - - - +
3439C ASP* 1.3 88.0 + - - +
3441C GLY* 2.9 22.7 + - - -
3442C ALA 3.8 5.8 + - - +
3444C THR* 3.3 13.4 + - - +
3519C GLU* 5.1 1.8 - - - +
3520C TYR* 3.3 31.0 - - + +
3521C ASN* 2.9 32.6 + - - -
3522C GLN* 3.4 25.5 + - - +
3524C GLU* 3.4 25.3 + - - +
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Residues in contact with ASP3439 (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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3339C ARG* 3.1 33.6 + - - +
3435C ARG* 2.9 24.2 + - - +
3436C ASN* 3.8 4.2 + - - +
3437C HIS 3.3 0.2 - - - -
3438C ARG* 1.3 106.7 + - - +
3440C ALA* 1.3 56.8 + - - +
3441C GLY 3.1 2.4 + - - -
3522C GLN* 3.6 11.5 + - - +
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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