Contacts of the strand formed by residues 3346 - 3351 (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 TYR3346 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3227C VAL* 4.1 1.6 - - + -
3228C SER* 3.3 26.1 + - - -
3231C VAL* 4.4 13.0 - - + -
3243C ALA* 3.2 29.6 - - + -
3245C SER* 2.6 44.2 + - - -
3249C VAL* 4.2 3.3 - - - +
3344C VAL* 5.2 0.2 - - + -
3345C PRO* 1.3 73.9 - - - +
3347C MET* 1.3 61.9 + - - +
3348C VAL* 3.8 21.1 - - + -
3433C VAL* 3.8 17.0 - - + -
3437C HIS* 3.3 47.6 - + + +
3443C PRO 2.9 8.5 + - - -
3444C THR* 3.3 7.2 - - + +
3445C TYR 3.0 24.8 + - - +
3503C PHE* 3.7 4.6 - - - -
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Residues in contact with MET3347 (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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3243C ALA 2.8 8.7 + - - -
3244C ILE* 3.2 22.9 - - + +
3245C SER 2.8 27.4 + - - +
3346C TYR* 1.3 72.6 - - - +
3348C VAL* 1.3 61.9 + - - +
3445C TYR* 3.3 11.4 - - + +
3447C TYR* 4.1 13.9 - - + -
3499C PHE 4.7 0.2 - - - +
3500C TRP* 3.7 44.2 - - + -
3503C PHE* 3.6 38.1 - - + -
3509C PRO* 4.1 9.6 - - + -
3517C TRP* 3.6 28.9 - - + -
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Residues in contact with VAL3348 (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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3245C SER* 3.5 6.3 - - - +
3249C VAL* 4.0 16.8 - - + -
3346C TYR* 3.8 39.5 - - + +
3347C MET* 1.3 78.8 - - - +
3349C GLY* 1.3 61.4 + - - +
3430C SER* 3.8 35.7 - - - +
3433C VAL* 4.8 1.8 - - + -
3434C ALA* 4.5 14.1 - - + -
3444C THR* 5.1 1.1 - - + -
3445C TYR 2.8 12.2 + - - +
3446C MET* 3.1 38.4 - - + +
3447C TYR* 3.4 2.2 + - - -
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Residues in contact with GLY3349 (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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3245C SER 3.0 10.3 + - - +
3247C SER* 2.8 25.2 + - - -
3248C GLY 4.7 0.2 + - - -
3348C VAL* 1.3 76.0 - - - +
3350C ILE* 1.3 67.8 + - - +
3430C SER* 4.5 2.8 + - - -
3446C MET* 5.2 1.1 - - - -
3447C TYR* 3.3 37.5 - - - -
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Residues in contact with ILE3350 (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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3247C SER* 3.9 2.7 - - - -
3349C GLY* 1.3 81.2 - - - +
3351C ASN* 1.3 73.8 + - - +
3354C GLU* 3.2 16.2 - - + +
3426C PHE* 4.0 11.9 - - + +
3427C GLY* 4.0 12.1 - - - +
3430C SER* 3.5 30.3 - - - +
3431C VAL* 6.0 0.2 - - + -
3446C MET* 5.4 2.0 - - + -
3447C TYR* 3.1 8.8 + - - +
3448C GLU* 3.2 24.2 - - + +
3449C PHE 2.8 22.7 + - - -
3539C LEU* 4.3 16.8 - - + -
3540C LYS* 3.8 28.9 - - + -
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Residues in contact with ASN3351 (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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3247C SER* 3.8 8.8 + - - -
3350C ILE* 1.3 85.0 - - - +
3352C LYS* 1.3 66.8 + - - +
3353C GLN 3.2 0.7 + - - -
3354C GLU* 2.7 28.9 + - - +
3447C TYR* 4.4 2.9 - - - -
3448C GLU* 4.5 2.5 - - - -
3449C PHE* 3.2 28.2 - - - +
3466C GLY 3.2 16.4 - - - +
3467C ASP 2.9 21.5 + - - +
3468C HIS* 4.1 0.4 - - - +
3469C GLY 3.5 5.9 - - - +
3470C ASP* 3.5 6.9 - - - +
3471C GLU* 3.0 32.8 + - - +
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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