Contacts of the strand formed by residues 65 - 77 (chain A) 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 LEU 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLY* 1.3 72.5 - - - -
66A LEU* 1.3 70.1 + - - +
67A LEU* 4.2 8.7 - - + -
438A ALA* 4.2 2.7 - - + -
439A SER* 4.0 11.0 - - - +
440A GLN* 3.5 46.5 - - + +
442A ASN* 3.7 32.3 - - + +
444A LEU* 3.9 15.0 - - + -
468A VAL* 4.9 7.9 - - + -
469A PRO 3.9 13.8 + - - +
470A LEU* 3.7 26.1 - - + -
471A THR* 2.9 27.7 + - - -
500A SO4 4.2 0.2 + - - -
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A HIS* 4.2 22.4 - - + +
64A GLY 4.6 3.4 - - - +
65A LEU* 1.3 73.8 - - - +
67A LEU* 1.3 62.1 + - - +
68A THR* 3.8 18.3 + - - +
437A VAL 3.3 2.9 - - - +
438A ALA* 3.5 2.3 - - - -
439A SER* 3.0 47.6 + - - +
471A THR* 3.3 36.3 - - + +
473A LYS* 3.9 24.5 - - + +
479A PHE* 4.3 5.8 - - + -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU* 4.2 13.5 - - + -
66A LEU* 1.3 74.9 - - - +
68A THR* 1.3 55.5 + - - +
436A LEU* 3.7 26.5 - - + +
437A VAL 3.3 2.5 - - - -
438A ALA* 3.8 30.7 - - + +
442A ASN* 5.0 2.5 - - - +
444A LEU* 5.2 3.6 - - + -
446A ALA* 4.0 26.7 - - + -
458A VAL* 5.2 0.7 - - + -
460A VAL* 4.4 6.7 - - + -
470A LEU* 3.8 32.8 - - + -
471A THR 2.8 10.1 + - - +
472A ILE* 3.2 13.3 - - + +
473A LYS 2.7 31.9 + - - +
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Residues in contact with THR 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A LEU* 3.8 21.1 - - - +
67A LEU* 1.3 73.1 - - - +
69A LEU* 1.3 76.3 + - - +
70A GLN* 3.5 18.9 + - - +
436A LEU* 3.3 5.1 - - - -
437A VAL* 2.9 41.6 + - - -
473A LYS* 3.5 29.5 - - + +
475A PRO* 4.3 3.8 - - + -
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 1.3 75.9 - - - +
70A GLN* 1.3 72.3 + - - +
71A PRO* 3.5 12.3 - - + +
434A VAL* 4.0 12.1 - - + -
435A GLY 3.9 6.5 - - - +
436A LEU* 3.8 6.2 - - + +
448A ALA* 3.6 31.0 - - + -
449A LEU 5.4 1.8 - - - +
450A MET* 5.7 1.8 - - + -
456A ALA* 4.2 12.8 - - + -
458A VAL* 4.6 10.5 - - + -
472A ILE* 5.3 1.1 - - + +
473A LYS 2.8 18.4 + - - +
474A ASP* 3.4 31.2 - - + +
475A PRO* 3.3 11.5 - - + +
494A TRP* 4.3 6.7 - - + -
496A ARG* 3.6 21.8 - - - +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A THR* 3.5 19.0 - - - +
69A LEU* 1.3 90.8 + - - +
71A PRO* 1.3 67.5 - - - +
72A GLU* 3.2 3.4 - - + +
73A GLN* 3.0 32.2 + - + +
434A VAL* 4.6 0.4 - - - -
435A GLY 3.0 27.7 + - - -
437A VAL* 3.6 32.0 - - + +
475A PRO* 4.6 6.5 - - - +
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Residues in contact with PRO 71 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LEU* 3.5 18.8 - - + +
70A GLN* 1.3 88.2 - - - +
72A GLU* 1.3 71.9 + - + +
73A GLN 3.1 5.0 + - - -
74A LYS* 2.5 32.9 + - - +
434A VAL* 3.9 15.3 - - + +
450A MET* 4.3 12.1 - - - -
475A PRO* 4.4 9.9 - - + -
496A ARG* 3.5 38.4 - - - +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLN* 3.1 2.7 + - + -
71A PRO* 1.3 91.6 - - + +
73A GLN* 1.3 57.3 + - - +
74A LYS* 3.7 15.9 + - - +
496A ARG* 5.7 0.5 + - - -
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLN* 3.0 26.5 + - + +
71A PRO 3.1 0.8 - - - -
72A GLU* 1.3 78.2 - - - +
74A LYS* 1.3 59.4 + - - +
75A PHE* 3.6 27.7 - - + -
434A VAL* 3.1 6.8 - - - -
435A GLY* 2.8 37.4 + - - +
437A VAL* 4.5 7.8 - - - +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A PRO* 2.5 34.7 + - - +
72A GLU* 3.7 14.3 + - - +
73A GLN* 1.3 74.7 - - - +
75A PHE* 1.3 71.0 + - - +
432A GLN* 3.2 28.7 - - - +
433A ARG 3.8 3.4 - - - -
434A VAL* 3.9 6.3 - - + +
450A MET* 3.7 32.8 - - - +
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Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A GLN* 3.6 43.5 - - + -
74A LYS* 1.3 78.9 - - - +
76A GLN* 1.3 75.6 + - - +
77A LYS 4.0 0.2 + - - -
374A HIS* 5.5 11.7 - + - +
432A GLN* 2.8 25.5 + - - +
433A ARG* 2.6 66.3 + - + +
434A VAL 3.8 1.8 - - - -
435A GLY* 3.7 13.5 - - - -
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Residues in contact with GLN 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE* 1.3 87.3 - - - +
77A LYS* 1.3 62.5 + - - +
78A VAL* 4.7 3.5 - - + +
328A HIS* 6.3 0.2 - - - +
371A LEU* 2.8 34.0 + - - +
374A HIS* 3.5 37.4 + - + +
375A VAL 3.1 24.4 + - - +
376A VAL* 3.9 15.7 - - + -
431A SER 4.0 0.3 - - - +
432A GLN* 3.5 1.9 - - - +
433A ARG* 3.0 35.8 + - - +
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Residues in contact with LYS 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A PHE 4.0 0.2 + - - -
76A GLN* 1.3 74.5 - - - +
78A VAL* 1.3 62.5 + - - +
376A VAL* 3.4 25.6 - - - +
430A GLY* 3.9 23.6 + - - +
431A SER 3.2 4.9 - - - +
432A GLN* 3.7 34.6 + - + +
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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