Contacts of the helix formed by residues 3449 - 3459 (chain D) in PDB entry 6X34
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 SER3449 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3445D TYR* 3.4 19.6 + - - +
3446D TRP 3.7 9.5 - - - +
3447D SER 4.5 2.0 - - - -
3448D LYS* 1.3 75.2 - - - +
3450D HIS* 1.3 64.8 + - - +
3451D ASN* 3.2 3.9 + - - -
3452D PHE* 3.4 34.7 + - - +
3453D LYS 3.5 8.0 + - - -
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Residues in contact with HIS3450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3446D TRP 5.5 0.2 - - - -
3447D SER 4.7 4.7 + - - +
3448D LYS 3.6 5.6 + - - +
3449D SER* 1.3 70.5 - - - +
3451D ASN* 1.3 64.0 + - - +
3453D LYS* 3.9 6.3 - - - +
3454D ARG* 3.2 25.6 + - - +
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Residues in contact with ASN3451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3449D SER* 3.2 3.5 - - - +
3450D HIS* 1.3 79.3 - - - +
3452D PHE* 1.3 71.8 + - + +
3454D ARG* 4.2 3.1 - - - +
3455D GLU* 3.1 26.7 + - - +
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Residues in contact with PHE3452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3398D GLU* 6.3 2.5 - - + -
3399D PHE* 6.4 2.0 - - + -
3445D TYR* 4.5 18.6 - - + +
3446D TRP* 5.8 3.9 - - + -
3449D SER* 3.4 28.5 + - - +
3450D HIS 3.4 0.4 - - - -
3451D ASN* 1.3 82.0 - - + +
3453D LYS* 1.3 64.0 + - - +
3455D GLU* 4.0 4.0 - - + +
3456D GLU* 3.1 24.8 + - - +
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Residues in contact with LYS3453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3446D TRP* 3.3 40.3 + - + +
3447D SER* 5.5 0.4 - - - -
3449D SER 3.5 6.5 + - - +
3450D HIS* 4.0 9.4 - - - +
3451D ASN 3.3 0.8 - - - -
3452D PHE* 1.3 76.9 - - - +
3454D ARG* 1.3 64.8 + - - +
3456D GLU* 3.5 12.7 + - - +
3457D GLN* 3.6 13.7 + - - +
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Residues in contact with ARG3454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3450D HIS 3.2 17.9 + - - +
3451D ASN* 4.3 3.6 - - - +
3453D LYS* 1.3 77.5 - - - +
3455D GLU* 1.3 61.8 + - - +
3457D GLN* 3.7 2.7 + - - +
3458D ASN* 3.3 24.1 + - - +
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Residues in contact with GLU3455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3399D PHE* 3.7 29.6 - - + +
3451D ASN 3.1 20.4 + - - +
3452D PHE* 4.3 5.4 - - + +
3454D ARG* 1.3 74.7 - - - +
3456D GLU* 1.3 63.8 + - - +
3458D ASN* 3.9 6.8 - - - +
3459D PHE* 3.6 19.6 + - - +
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Residues in contact with GLU3456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3399D PHE* 5.6 2.0 - - - -
3403D CYS* 4.3 13.4 - - + +
3446D TRP* 4.3 26.0 - - + -
3452D PHE 3.1 18.9 + - - +
3453D LYS* 3.8 5.8 - - - +
3454D ARG 3.3 0.6 - - - -
3455D GLU* 1.3 79.7 - - - +
3457D GLN* 1.3 61.6 + - - +
3458D ASN 3.4 0.5 + - - -
3459D PHE* 3.6 7.4 + - - +
3460D VAL* 3.3 16.0 + - - +
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Residues in contact with GLN3457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3453D LYS 3.6 11.9 + - - +
3454D ARG* 4.5 2.7 - - - +
3456D GLU* 1.3 76.9 - - - +
3458D ASN* 1.3 63.0 + - - +
3459D PHE 3.4 0.2 - - - -
3460D VAL* 3.6 22.2 + - + +
3461D VAL* 4.2 5.7 + - - +
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Residues in contact with ASN3458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3454D ARG 3.3 19.9 + - - +
3455D GLU* 4.0 9.0 - - - +
3456D GLU 3.2 1.2 - - - -
3457D GLN* 1.3 79.8 - - - +
3459D PHE* 1.3 60.4 + - - +
3460D VAL 3.5 0.5 + - - -
3461D VAL* 3.8 16.2 + - - +
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Residues in contact with PHE3459 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3399D PHE* 4.6 2.7 - - + +
3400D SER* 3.7 43.5 - - - -
3403D CYS* 3.6 30.1 - - + -
3404D ARG* 4.6 10.8 - - + -
3455D GLU 3.6 11.0 + - - +
3456D GLU 3.6 1.6 + - - +
3457D GLN 3.4 0.4 - - - -
3458D ASN* 1.3 76.7 - - - +
3460D VAL* 1.3 64.8 + - - +
3461D VAL 3.4 7.6 - - - +
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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