Contacts of the strand formed by residues 3444 - 3449 (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 THR3444 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3346C TYR* 3.3 11.9 - - + +
3348C VAL* 5.1 2.2 - - + -
3434C ALA* 3.7 36.8 - - + +
3437C HIS* 3.3 17.9 - - + -
3438C ARG* 3.3 11.3 + - - -
3442C ALA 3.1 15.2 + - - -
3443C PRO* 1.3 71.7 - - - +
3445C TYR* 1.3 71.2 + - - +
3519C GLU* 2.8 11.3 + - - +
3520C TYR* 2.8 46.8 + - + -
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Residues in contact with TYR3445 (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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3346C TYR 3.0 8.9 + - - +
3347C MET* 3.3 10.0 - - + -
3348C VAL 2.8 26.8 + - - -
3443C PRO* 4.6 10.2 - - + +
3444C THR* 1.3 82.4 - - - +
3446C MET* 1.3 67.3 + - - +
3503C PHE* 3.7 18.8 - + - -
3507C GLY 3.4 21.3 + - - -
3508C ASN* 3.1 28.2 + - - +
3509C PRO* 3.6 24.7 - - + -
3510C ASN* 4.6 2.2 + - - -
3517C TRP* 4.0 27.6 - + + +
3518C PRO 3.6 15.3 - - - -
3519C GLU* 3.5 34.5 - - + +
3520C TYR* 4.0 3.4 - - - -
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Residues in contact with MET3446 (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* 3.1 20.4 - - + +
3349C GLY* 5.1 1.8 - - - +
3350C ILE* 5.4 1.1 - - + -
3430C SER* 3.9 26.9 - - - +
3431C VAL* 3.8 21.1 - - + -
3434C ALA* 3.5 26.0 - - + -
3445C TYR* 1.3 79.2 - - - +
3447C TYR* 1.3 61.7 + - - +
3517C TRP* 3.1 12.4 + - - +
3520C TYR* 3.6 35.5 - - + +
3525C GLY 4.8 1.2 + - - -
3526C TYR* 3.2 19.1 - - + +
3527C LEU 2.9 20.4 + - - -
3539C LEU* 3.8 22.2 - - + -
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Residues in contact with TYR3447 (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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3244C ILE* 5.1 0.4 - - + -
3245C SER 4.9 0.4 - - - -
3246C GLU* 3.1 38.6 - - + +
3247C SER 4.5 0.3 + - - -
3347C MET* 4.1 12.1 - - + -
3348C VAL 3.4 3.7 + - - +
3349C GLY* 3.3 28.2 - - - -
3350C ILE* 3.1 38.0 + - - +
3351C ASN* 4.4 2.2 + - - -
3446C MET* 1.3 77.0 - - - +
3448C GLU* 1.3 62.9 + - - +
3449C PHE* 3.7 22.2 - + + -
3471C GLU* 4.2 9.6 - - + +
3500C TRP* 3.6 32.5 - + - -
3517C TRP* 3.6 21.3 - + + -
3526C TYR* 4.6 3.8 - - - -
3527C LEU 3.1 14.6 - - - +
3529C ILE* 3.9 13.9 - - + -
3539C LEU* 4.4 5.1 - - - +
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Residues in contact with GLU3448 (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* 3.2 19.2 - - + +
3352C LYS* 3.6 48.3 + - + +
3447C TYR* 1.3 75.9 - - - +
3449C PHE* 1.3 62.1 + - - +
3450C GLN* 3.6 4.2 + - + +
3526C TYR* 4.0 25.0 + - + -
3527C LEU 3.0 7.2 + - - +
3528C GLN* 3.5 12.3 + - - +
3529C ILE 3.0 22.4 + - - -
3539C LEU* 3.9 21.9 - - + +
3540C LYS* 4.2 16.6 + - - -
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Residues in contact with PHE3449 (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 2.8 9.6 + - - +
3351C ASN* 3.2 24.1 - - - +
3352C LYS* 2.7 30.3 + - - +
3447C TYR* 3.7 11.2 - + + -
3448C GLU* 1.3 70.3 - - - +
3450C GLN* 1.3 56.8 + - - +
3451C TYR* 3.6 38.6 - + + -
3453C PRO* 5.2 0.2 - - + -
3466C GLY* 3.9 1.7 - - - -
3470C ASP* 3.6 11.2 - - + -
3471C GLU* 3.5 42.2 - - + -
3474C SER* 4.0 22.7 - - - -
3492C LEU* 4.2 9.0 - - + -
3496C VAL* 4.8 3.4 - - + -
3529C ILE* 3.6 35.7 - - + -
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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