Contacts of the strand formed by residues 65 - 77 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64C GLY* 1.3 71.4 - - - +
66C LEU* 1.3 75.5 + - - +
67C LEU* 4.1 7.6 - - + -
438C ALA* 4.0 3.4 - - + -
439C SER 4.0 8.3 - - - +
440C GLN* 3.6 34.2 - - + +
442C ASN* 3.5 46.7 - - + +
444C LEU* 3.9 17.5 - - + -
468C VAL* 5.0 7.9 - - + -
469C PRO 4.1 10.7 + - - +
470C LEU* 3.6 25.9 - - + -
471C THR* 3.0 25.1 + - - -
499C SO4 5.3 0.4 + - - -
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Residues in contact with LEU 66 (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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60C HIS* 3.8 33.2 - - + +
64C GLY 3.4 4.2 + - - +
65C LEU* 1.3 74.5 - - - +
67C LEU* 1.3 62.4 + - - +
68C THR* 3.8 16.1 + - - +
437C VAL 3.4 3.5 - - - +
438C ALA* 3.6 2.1 - - - -
439C SER* 3.1 45.8 + - - +
471C THR* 3.3 24.9 - - + +
473C LYS* 4.1 23.3 - - + +
479C PHE* 4.4 3.8 - - + -
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Residues in contact with LEU 67 (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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65C LEU* 4.1 14.1 - - + -
66C LEU* 1.3 78.4 - - - +
68C THR* 1.3 55.1 + - - +
69C LEU 4.1 0.2 - - - -
436C LEU* 3.9 24.2 - - + +
437C VAL 3.3 3.4 - - - +
438C ALA* 3.9 24.9 - - + +
442C ASN* 5.0 1.8 - - - +
444C LEU* 5.5 2.0 - - + -
446C ALA* 4.0 28.9 - - + -
458C VAL* 5.0 0.9 - - + -
460C VAL* 4.5 7.6 - - + -
470C LEU* 3.6 31.9 - - + -
471C THR 2.7 11.4 + - - +
472C ILE* 3.1 13.9 - - + +
473C LYS 2.7 31.7 + - - -
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Residues in contact with THR 68 (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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66C LEU* 3.8 19.6 - - - +
67C LEU* 1.3 74.0 + - - +
69C LEU* 1.3 74.8 + - - +
70C GLN* 3.5 19.3 - - - +
436C LEU* 3.4 5.2 - - - -
437C VAL* 2.9 42.8 + - - +
473C LYS* 3.4 32.9 - - + +
475C PRO* 4.1 5.2 - - + -
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Residues in contact with LEU 69 (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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68C THR* 1.3 70.2 - - - +
70C GLN* 1.3 71.1 + - - +
71C PRO* 3.4 24.8 - - + +
434C VAL* 3.8 16.6 - - + -
435C GLY 3.6 4.0 - - - +
436C LEU* 3.8 7.5 - - + +
448C ALA* 3.5 31.2 - - + -
449C LEU 5.3 1.6 - - - +
450C MET* 4.4 4.0 - - + -
456C ALA* 4.6 8.5 - - + -
458C VAL* 4.7 4.5 - - + -
472C ILE* 5.5 0.7 - - + -
473C LYS 2.8 17.4 + - - +
474C ASP* 4.0 14.1 - - + +
475C PRO* 3.4 15.0 - - + +
494C TRP* 4.3 14.6 - - + -
496C ARG* 3.7 31.9 - - - +
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Residues in contact with GLN 70 (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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68C THR* 3.5 26.4 - - - +
69C LEU* 1.3 87.9 + - - +
71C PRO* 1.3 61.6 - - - +
72C GLU* 2.9 12.0 + - + -
73C GLN* 3.1 33.8 + - + +
434C VAL* 4.6 0.4 - - - -
435C GLY 2.7 27.4 + - - +
437C VAL* 3.6 23.8 - - + +
475C PRO* 4.3 8.3 - - - +
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Residues in contact with PRO 71 (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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69C LEU* 3.4 16.4 - - + +
70C GLN* 1.3 88.6 - - - +
72C GLU* 1.3 75.0 + - + +
73C GLN 3.7 0.7 - - - -
74C LYS* 3.0 36.9 + - - +
434C VAL* 4.0 7.5 - - + +
450C MET* 3.5 30.3 - - + -
475C PRO* 4.9 8.3 - - + -
496C ARG* 3.5 29.6 - - - +
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Residues in contact with GLU 72 (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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70C GLN* 2.9 3.5 + - + -
71C PRO* 1.3 97.3 - - + +
73C GLN* 1.4 59.9 + - - +
74C LYS* 3.4 18.5 + - - +
496C ARG* 5.6 0.7 + - - -
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Residues in contact with GLN 73 (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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70C GLN* 3.1 27.4 + - + +
72C GLU* 1.4 72.7 - - - +
74C LYS* 1.3 61.9 + - - +
75C PHE* 3.8 25.0 - - + -
434C VAL* 3.2 7.3 - - - +
435C GLY* 3.0 43.9 + - - -
437C VAL* 3.9 11.6 - - - +
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Residues in contact with LYS 74 (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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71C PRO* 3.0 31.4 + - - +
72C GLU* 3.4 17.9 + - - +
73C GLN* 1.3 73.4 - - - +
75C PHE* 1.3 69.6 + - - +
432C GLN* 3.6 30.3 + - - +
433C ARG 3.7 3.4 - - - -
434C VAL* 4.2 7.0 - - + +
450C MET* 3.6 28.3 - - - +
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Residues in contact with PHE 75 (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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73C GLN* 3.8 32.1 - - + -
74C LYS* 1.3 78.1 - - - +
76C GLN* 1.3 76.6 + - - +
77C LYS 3.9 0.3 + - - -
374C HIS* 5.4 14.1 - + - +
432C GLN* 2.6 27.1 + - - +
433C ARG* 2.7 58.7 + - + +
434C VAL 3.9 3.8 - - - -
435C GLY* 3.8 21.3 - - - -
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Residues in contact with GLN 76 (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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75C PHE* 1.3 86.2 - - - +
77C LYS* 1.3 62.4 + - - +
78C VAL* 4.1 4.1 + - + +
371C LEU* 2.7 36.6 + - - +
374C HIS* 3.5 33.4 + - + +
375C VAL 3.3 28.1 + - - +
376C VAL* 4.1 13.5 - - + -
431C SER 4.0 0.2 - - - +
432C GLN* 3.4 0.5 - - - -
433C ARG* 2.9 39.1 + - - +
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Residues in contact with LYS 77 (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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75C PHE 3.9 0.4 + - - -
76C GLN* 1.3 73.8 - - - +
78C VAL* 1.3 62.2 + - - +
79C LYS 3.9 0.2 + - - -
376C VAL* 3.4 24.8 - - - +
430C GLY* 4.0 22.7 - - - +
431C SER 3.2 4.5 - - - +
432C GLN* 3.8 36.8 - - + +
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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