Contacts of the strand formed by residues 73 - 80 (chain D) in PDB entry 4GID
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 GLN 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67D THR* 3.2 3.2 - - - -
68D VAL* 2.8 48.8 + - + +
71D PRO* 3.9 7.2 + - + +
72D PRO* 1.3 75.1 - - - +
74D THR* 1.3 64.5 + - - +
75D LEU* 3.6 5.9 + - + +
99D TYR 3.8 5.1 - - - +
100D TYR* 3.5 14.7 - - - -
101D GLN* 2.8 53.8 + - - +
104D LEU* 3.9 22.3 + - - +
105D SER* 4.2 9.3 - - - +
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Residues in contact with THR 74 (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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65D GLU* 3.6 38.4 + - + +
66D MET 3.5 6.1 - - - +
67D THR* 3.9 13.7 - - + +
72D PRO* 3.9 4.0 + - - +
73D GLN* 1.3 71.5 - - - +
75D LEU* 1.3 73.1 + - - +
98D ARG* 3.4 34.8 + - - +
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Residues in contact with LEU 75 (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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65D GLU* 3.7 1.6 - - - +
66D MET* 2.8 36.0 + - - +
68D VAL* 3.7 27.4 - - + -
73D GLN* 3.9 9.4 - - + +
74D THR* 1.3 83.8 - - - +
76D ASN* 1.3 65.9 + - - +
77D ILE* 3.7 14.2 + - + +
88D VAL* 4.1 28.5 - - + -
89D GLY 5.1 0.4 - - - +
98D ARG* 3.8 23.6 - - + +
99D TYR* 4.2 20.6 - - - +
100D TYR* 4.2 11.7 - - + +
164D GLU* 3.4 11.7 - - + +
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Residues in contact with ASN 76 (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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63D TYR* 3.5 33.2 + - + -
64D VAL 3.7 2.2 - - - -
65D GLU* 4.3 19.8 + - - +
75D LEU* 1.3 71.6 + - - +
77D ILE* 1.3 61.6 + - - +
78D LEU 4.1 0.2 - - - -
98D ARG* 3.0 28.2 + - - +
162D ASN* 2.8 31.5 - - - +
163D TRP* 3.6 2.7 - - - -
164D GLU* 2.8 40.3 + - - +
165D GLY 3.3 5.4 + - - -
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Residues in contact with ILE 77 (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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63D TYR* 3.5 3.1 - - - +
64D VAL* 2.8 41.3 + - + +
66D MET* 3.6 29.4 - - + -
68D VAL* 6.0 0.7 - - + -
75D LEU* 3.8 23.6 - - + +
76D ASN* 1.3 79.6 - - - +
78D LEU* 1.3 62.8 + - - +
79D VAL 3.5 0.5 + - - -
86D PHE* 3.9 10.5 - - + -
88D VAL* 3.9 19.3 - - + -
165D GLY* 3.5 16.8 - - - +
166D ILE 3.5 8.1 - - - +
167D LEU* 3.4 39.3 - - + +
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Residues in contact with LEU 78 (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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61D GLY* 3.6 24.9 - - - -
62D TYR 3.5 11.2 - - - +
63D TYR* 3.7 5.6 - - - +
76D ASN 4.1 1.0 + - - -
77D ILE* 1.3 71.2 - - - +
79D VAL* 1.3 67.7 + - - +
80D ASP* 3.6 12.4 + - + -
163D TRP* 3.6 41.4 - - + +
165D GLY 2.8 16.9 + - - +
166D ILE* 3.5 26.8 - - + -
167D LEU* 2.8 30.0 + - - +
277D SER 5.7 0.7 - - - +
278D GLY* 4.6 4.7 - - - -
501D 0GH 3.9 25.4 - - + -
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Residues in contact with VAL 79 (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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54D LEU* 4.7 7.9 - - + -
62D TYR* 2.9 19.7 + - + +
64D VAL* 3.8 34.1 - - + +
77D ILE 3.9 1.1 - - - +
78D LEU* 1.3 77.1 - - - +
80D ASP* 1.3 55.5 + - - +
167D LEU* 4.2 8.1 - - + -
169D LEU* 3.3 28.3 - - + -
200D LEU* 3.9 30.7 - - + -
202D LEU* 6.0 2.0 - - + +
222D MET* 3.9 14.6 - - + -
277D SER* 2.8 27.9 + - - +
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Residues in contact with ASP 80 (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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78D LEU* 3.6 5.6 + - + -
79D VAL* 1.3 74.6 - - - +
81D THR* 1.3 60.1 + - - +
82D GLY* 2.8 22.6 + - - -
83D SER* 2.4 30.1 + - - +
166D ILE* 3.6 24.4 - - + +
167D LEU 3.0 10.9 + - - +
168D GLY* 3.4 2.3 - - - -
169D LEU* 2.8 26.6 + - - -
276D ASP* 2.9 16.3 - - - +
277D SER* 3.3 1.6 - - - -
278D GLY* 3.3 5.5 + - - +
501D 0GH 3.6 22.2 - - - +
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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