Contacts of the strand formed by residues 61 - 68 (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 GLY 61 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ARG 4.0 0.2 - - - +
56D GLY* 3.3 21.3 - - - -
57D LYS 3.2 7.9 + - - -
60D GLN* 1.3 80.8 - - - +
62D TYR* 1.3 65.8 + - - -
63D TYR* 4.2 6.1 - - - -
78D LEU* 3.6 18.4 - - - -
161D SER 5.3 0.7 - - - +
163D TRP* 4.8 1.4 - - - -
501D 0GH 3.2 20.1 - - - -
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Residues in contact with TYR 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LEU* 4.7 8.3 - - + -
55D ARG 3.3 13.2 - - - +
56D GLY 4.0 5.8 - - - -
57D LYS 3.8 20.6 - - - -
58D SER 3.4 9.4 + - - -
61D GLY* 1.3 73.9 - - - -
63D TYR* 1.3 61.5 + - - +
78D LEU* 3.5 7.2 - - - +
79D VAL* 2.9 29.9 + - + +
202D LEU* 3.7 43.1 - - + -
203D CYS 3.2 31.0 + - - -
204D GLY* 3.5 0.9 - - - -
219D GLY 3.2 29.4 - - - -
277D SER 5.4 1.7 + - - +
383D ALA* 4.7 0.4 - - + -
387D GLU* 2.9 27.9 + - + -
501D 0GH 4.1 21.1 - + - -
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Residues in contact with TYR 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASN 4.1 0.3 - - - +
54D LEU* 3.5 10.6 - - - +
55D ARG* 2.9 85.2 + - + +
56D GLY* 3.9 7.0 - - - -
61D GLY 4.2 6.5 - - - -
62D TYR* 1.3 76.5 - - - +
64D VAL* 1.3 63.8 + - - +
76D ASN* 3.5 36.3 + - + -
77D ILE 3.2 22.2 - - - +
78D LEU* 3.7 4.3 - - - +
79D VAL* 4.3 0.9 - - - +
161D SER 3.4 23.1 - - - -
162D ASN* 3.5 23.4 + - + +
163D TRP* 3.9 16.8 - + + -
214D VAL* 4.3 5.5 - - + +
215D LEU* 4.3 0.9 - - - +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASN* 4.0 24.5 - - + +
54D LEU* 3.6 16.2 - - + -
63D TYR* 1.3 75.9 - - - +
65D GLU* 1.3 73.9 + - + +
66D MET* 3.6 21.6 + - + -
76D ASN* 3.7 2.4 - - - -
77D ILE* 2.8 40.1 + - + +
79D VAL* 3.8 14.8 - - + +
135D ILE* 4.2 15.7 - - + -
137D HIS* 5.6 1.6 - - + +
167D LEU* 4.7 1.3 - - + -
222D MET* 3.8 16.4 - - + -
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Residues in contact with GLU 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D ASN 4.6 3.4 + - - +
55D ARG* 5.9 0.7 + - - -
63D TYR* 5.3 0.2 - - - -
64D VAL* 1.3 76.3 - - - +
66D MET* 1.3 69.2 + - - +
74D THR* 3.6 30.2 + - + +
75D LEU 3.7 4.5 - - - +
76D ASN* 4.3 14.6 + - - +
98D ARG* 5.2 0.9 + - - -
135D ILE* 3.6 11.6 - - - +
136D PRO* 3.3 38.8 - - + +
137D HIS* 4.6 19.5 + - + -
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Residues in contact with MET 66 (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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64D VAL* 4.1 9.6 - - + -
65D GLU* 1.3 81.0 - - - +
67D THR* 1.3 66.7 + - - +
68D VAL* 5.2 4.0 - - + -
73D GLN 3.8 0.2 - - - +
74D THR* 3.5 4.0 - - - +
75D LEU* 2.8 32.9 + - + +
77D ILE* 3.6 37.7 - - + -
86D PHE* 3.9 17.7 - - + -
133D VAL* 3.4 32.8 - - + -
134D SER 3.4 9.0 - - - +
135D ILE* 4.0 14.8 - - + -
136D PRO* 3.8 2.0 - - - -
167D LEU* 4.1 15.5 - - + -
184D PHE* 3.8 23.6 - - + -
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Residues in contact with THR 67 (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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66D MET* 1.3 78.2 - - - +
68D VAL* 1.3 65.3 + - - +
72D PRO* 3.7 27.8 - - + +
73D GLN 3.2 6.7 - - - -
74D THR* 3.9 18.6 - - - +
132D LEU 4.5 0.2 - - - -
133D VAL* 3.2 5.2 - - - +
134D SER* 3.0 46.5 + - - +
136D PRO* 3.8 22.2 - - + -
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D MET* 5.2 3.1 - - + -
67D THR* 1.3 81.9 - - - +
69D GLY* 1.3 64.1 + - - +
73D GLN* 2.8 44.2 + - + +
75D LEU* 3.7 21.1 - - + -
77D ILE* 6.0 0.7 - - + -
86D PHE* 4.1 19.1 - - + -
88D VAL* 5.2 2.9 - - + -
100D TYR* 3.7 29.2 - - + -
132D LEU 3.3 5.6 - - - +
133D VAL* 4.0 17.7 - - + -
147D ILE* 4.3 14.6 - - + -
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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
------------------------------------------------------------
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