Contacts of the strand formed by residues 401 - 404 (chain D) in PDB entry 1M7X
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 ALA 401 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D ASN* 4.4 4.9 - - - +
332D VAL 3.1 3.2 + - - -
333D ILE* 3.3 23.7 - - + -
334D LEU 2.8 29.9 + - - -
394D ILE* 5.7 0.9 - - - -
399D ILE* 3.3 14.3 + - - +
400D ASP* 1.3 81.8 - - - +
402D LEU* 1.3 54.2 + - - +
453D ALA* 5.0 2.2 - - - -
454D VAL* 3.1 34.5 - - + +
456D MET* 4.5 3.4 - - + -
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Residues in contact with LEU 402 (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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333D ILE* 4.4 2.9 - - - -
334D LEU* 3.4 18.8 - - + +
336D TRP* 4.0 31.0 - - + -
390D ALA* 3.6 35.2 - - + -
393D TRP* 4.4 9.6 - - + -
394D ILE* 4.1 15.7 - - + +
399D ILE* 3.2 30.7 - - + -
401D ALA* 1.3 74.1 - - - +
403D ARG* 1.3 60.1 + - - +
404D VAL* 5.3 1.7 - - + +
446D LEU* 4.4 7.9 - - + -
454D VAL 3.3 5.9 + - - +
455D THR* 3.3 13.9 - - + -
456D MET* 2.9 26.2 + - - +
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Residues in contact with ARG 403 (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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247D GLU* 4.9 0.2 + - - -
285D GLU* 2.7 28.1 + - - +
300D TYR* 3.4 9.3 + - - -
333D ILE* 4.0 15.0 - - + +
334D LEU 3.0 7.6 + - - +
335D ASP* 2.7 46.2 + - - +
336D TRP 2.7 29.4 + - - +
402D LEU* 1.3 74.7 - - - +
404D VAL* 1.3 64.3 + - - +
405D ASP* 3.6 30.2 + - - +
456D MET* 3.5 20.0 - - + +
457D ALA 5.1 0.4 - - - +
458D GLU* 3.8 16.6 + - - +
481D TRP* 3.1 47.0 - - + +
525D HIS* 4.7 3.8 + - - -
526D ASP* 5.2 4.4 + - - -
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Residues in contact with VAL 404 (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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336D TRP* 3.5 39.0 - - + +
338D PRO* 4.0 19.5 - - + -
339D GLY 5.3 0.4 - - - +
402D LEU* 5.3 2.5 - - + +
403D ARG* 1.3 78.7 - - - +
405D ASP* 1.3 73.7 + - - +
407D VAL* 3.9 13.2 - - + +
410D MET* 4.4 9.9 - - - -
439D LEU* 4.8 4.9 - - + -
455D THR* 6.1 2.0 - - + -
456D MET 2.9 10.9 + - - +
457D ALA* 3.5 3.5 - - - -
458D GLU* 3.3 23.6 + - - +
477D PHE* 4.0 23.1 - - + -
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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