Contacts of the strand formed by residues 3525 - 3529 (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 GLY3525 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3446C MET 4.8 0.7 + - - +
3518C PRO* 3.8 22.8 - - - +
3519C GLU 4.1 9.2 + - - -
3520C TYR* 3.3 25.3 - - - +
3523C LYS* 3.2 7.0 + - - +
3524C GLU* 1.3 80.8 - - - +
3526C TYR* 1.3 58.7 + - - -
3536C ALA 3.2 12.1 - - - -
3537C GLN* 4.1 7.0 - - - -
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Residues in contact with TYR3526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3446C MET* 3.2 28.3 - - + +
3448C GLU* 4.0 18.2 + - + -
3517C TRP* 4.6 2.2 - - - +
3518C PRO* 3.7 8.8 - - - +
3520C TYR* 4.8 0.7 - - + -
3524C GLU 3.8 9.4 - - - +
3525C GLY* 1.3 74.3 - - - +
3527C LEU* 1.3 68.4 + - - +
3528C GLN* 3.5 33.6 + - + -
3535C ALA* 3.4 4.2 - - - +
3536C ALA* 2.9 43.6 + - + +
3537C GLN 3.5 30.2 + - - -
3538C LYS 5.1 0.3 + - - -
3539C LEU* 3.6 48.0 - - + +
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Residues in contact with LEU3527 (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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3446C MET 2.9 9.3 + - - -
3447C TYR* 3.1 5.7 - - - +
3448C GLU 3.0 24.4 + - - -
3499C PHE* 3.6 24.2 - - + -
3515C PRO* 5.0 3.6 - - + -
3516C HIS 3.8 21.1 - - - +
3517C TRP* 3.5 47.7 - - + +
3526C TYR* 1.3 75.4 - - - +
3528C GLN* 1.3 61.9 + - - +
3529C ILE* 3.4 13.3 + - + +
3533C THR* 3.7 21.1 - - + -
3534C GLN* 3.7 25.6 - - - -
3535C ALA* 3.9 1.8 - - - +
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Residues in contact with GLN3528 (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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3352C LYS* 6.0 1.2 - - - +
3448C GLU* 3.5 16.9 + - - +
3450C GLN* 5.9 4.7 - - + +
3526C TYR* 3.5 34.7 + - + -
3527C LEU* 1.3 69.2 - - - +
3529C ILE* 1.3 60.8 + - - +
3532C ASN 3.8 2.0 - - - +
3533C THR* 3.2 26.2 - - - +
3534C GLN* 2.7 50.7 + - - +
3536C ALA* 3.7 18.0 - - + +
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Residues in contact with ILE3529 (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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3447C TYR* 3.9 28.7 - - + -
3448C GLU 3.0 9.0 + - - +
3449C PHE* 3.6 28.5 - - + -
3450C GLN* 2.8 32.1 + - - +
3492C LEU* 4.0 5.8 - - + -
3495C MET* 3.9 19.7 - - + -
3496C VAL* 4.2 7.6 - - + -
3499C PHE* 5.0 4.3 - - + -
3500C TRP* 4.3 22.7 - - + -
3517C TRP* 4.3 2.2 - - + -
3527C LEU* 3.7 32.5 - - + +
3528C GLN* 1.3 72.5 - - - +
3530C GLY* 1.3 62.2 + - - +
3532C ASN 4.6 0.7 - - - -
3533C THR* 3.7 3.6 - - + -
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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