Contacts of the strand formed by residues 488 - 494 (chain D) in PDB entry 3GXM
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 SER 488 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D SER 3.3 11.9 - - - -
43D THR* 4.1 12.3 - - - -
357D TRP* 4.1 3.6 - - - -
461D LEU* 3.6 4.0 - - - +
462D ASN* 3.0 24.8 + - - +
484D SER* 3.9 6.4 + - - -
485D PRO* 2.4 48.9 + - - +
487D TYR* 1.3 78.5 - - - +
489D ILE* 1.3 65.3 + - - +
490D HIS* 4.0 8.4 + - - -
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Residues in contact with ILE 489 (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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40D TYR 3.6 0.2 - - - +
42D SER* 2.9 40.7 + - - +
364D SER* 3.7 29.4 - - - -
419D HIS* 3.5 26.9 - - + +
422D HIS* 3.2 51.1 - - + +
423D PHE* 4.1 1.6 - - + -
459D VAL* 3.8 16.6 - - + -
460D VAL 3.3 17.7 - - - +
461D LEU* 4.0 11.4 - - + -
488D SER* 1.3 76.1 - - - +
490D HIS* 1.3 66.1 + - - +
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Residues in contact with HIS 490 (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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39D ARG* 3.5 23.8 + - + -
40D TYR 3.2 6.5 - - - +
41D GLU* 3.2 31.5 + - + +
422D HIS* 3.9 1.6 - - - -
458D VAL 3.7 0.3 - - - +
459D VAL* 3.1 8.1 - - - +
460D VAL* 2.8 43.2 + - + +
483D ILE 3.3 25.1 + - - -
484D SER* 4.4 5.3 - - - -
485D PRO* 3.5 14.1 - - + +
488D SER* 4.0 3.7 + - - -
489D ILE* 1.3 87.8 - - - +
491D THR* 1.3 60.5 + - - +
492D TYR* 2.6 39.9 + - + -
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Residues in contact with THR 491 (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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38D SER 3.7 0.5 - - - +
39D ARG* 3.3 5.4 - - - +
40D TYR* 2.8 40.4 + - - +
422D HIS* 2.9 41.6 + - - +
426D PHE* 3.7 30.0 - - + -
457D VAL* 3.6 28.5 - - + -
458D VAL 3.3 4.3 - - - +
459D VAL* 4.1 3.6 - - + +
490D HIS* 1.3 73.4 + - - +
492D TYR* 1.3 66.5 + - - +
493D LEU* 4.3 4.5 - - + -
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Residues in contact with TYR 492 (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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37D PHE* 4.1 16.6 - + - -
38D SER 3.3 4.0 - - - +
39D ARG* 3.8 17.9 - - + -
456D ALA 3.9 0.2 - - - +
457D VAL* 3.2 6.9 - - - +
458D VAL* 2.8 41.9 + - + +
460D VAL* 4.1 17.7 - - + -
470D LEU* 6.1 0.4 - - + -
472D ILE* 4.3 11.9 - - + -
480D LEU* 4.0 17.0 - - + -
482D THR* 2.6 44.6 + - + +
483D ILE 4.0 1.4 + - - -
484D SER* 5.4 1.2 - - - -
490D HIS* 2.6 44.4 + - + -
491D THR* 1.3 75.5 - - - +
493D LEU* 1.3 61.6 + - - +
494D TRP* 3.9 21.8 - - + -
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Residues in contact with LEU 493 (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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32D PRO* 3.5 9.2 - - + +
37D PHE* 3.4 1.6 - - - +
38D SER* 2.9 46.1 + - - +
40D TYR* 3.4 38.8 - - + -
426D PHE* 3.7 36.8 - - + -
451D HIS* 4.3 14.1 - - + -
456D ALA 3.4 7.2 - - - +
457D VAL* 4.0 16.6 - - + -
491D THR* 4.3 3.4 - - + +
492D TYR* 1.3 76.0 - - - +
494D TRP* 1.3 65.6 + - - +
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Residues in contact with TRP 494 (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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32D PRO* 3.8 8.3 - - - +
36D THR 3.7 16.2 - - - +
37D PHE* 4.2 2.0 - - - -
56D ILE* 3.8 10.8 - - + -
69D LEU* 4.5 6.5 - - + -
455D SER* 3.2 5.2 - - - -
456D ALA* 3.0 52.9 + - + +
458D VAL* 3.6 28.3 - - + -
472D ILE* 3.9 18.8 - - + -
474D ASP* 2.8 39.9 + - + -
477D VAL* 3.6 16.1 - - + +
480D LEU* 3.8 32.8 - - + -
492D TYR* 3.9 18.4 - - + -
493D LEU* 1.3 83.5 - - - +
495D HIS* 1.3 85.9 + - - +
496D ARG* 4.2 1.3 - - + -
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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