Contacts of the strand formed by residues 95 - 100 (chain D) in PDB entry 3GZN
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 95 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67D LEU 3.0 21.3 + - - +
68D ASP* 3.4 28.3 + - - +
69D THR* 4.6 3.6 - - - +
70D CYS 3.6 15.4 + - - +
71D LYS* 3.7 16.5 - - + -
72D VAL* 3.2 24.3 + - - +
94D ARG* 1.3 91.4 - - - +
96D ILE* 1.3 61.6 + - - +
97D HIS* 4.5 7.5 - - + +
140D ASN* 3.5 25.9 + - - +
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Residues in contact with ILE 96 (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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72D VAL* 3.4 12.3 - - + +
74D VAL* 4.0 11.2 - - + -
85D LEU* 3.8 26.5 - - + +
88D LEU* 3.9 26.9 - - + -
89D ALA* 4.0 12.1 - - - +
93D PHE* 3.9 23.3 - - + +
94D ARG 3.2 10.9 + - - +
95D GLN* 1.3 76.8 - - - +
97D HIS* 1.3 71.9 + - - +
139D CYS* 4.5 9.9 - - - -
140D ASN 3.2 4.3 + - - +
141D VAL* 3.2 13.8 - - + -
142D VAL 2.7 31.4 + - - -
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Residues in contact with HIS 97 (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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71D LYS* 4.9 13.8 - - + +
72D VAL 3.0 8.0 + - - -
73D LEU* 3.7 19.7 - - + -
74D VAL* 2.8 30.5 + - - +
95D GLN* 4.5 6.6 - - - +
96D ILE* 1.3 90.2 - - - +
98D VAL* 1.3 64.6 + - - +
141D VAL* 5.2 0.2 - - - -
142D VAL* 3.3 29.4 - - + +
144D HIS* 2.9 28.2 + + + -
155D PHE* 5.5 1.6 - + - -
158D GLN* 4.7 7.9 - - - -
159D PHE* 3.6 25.0 - + + -
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Residues in contact with VAL 98 (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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74D VAL* 3.2 18.4 - - + +
76D GLY 5.1 3.4 - - - +
77D ALA* 5.2 4.7 - - + -
85D LEU* 3.4 42.6 - - + -
97D HIS* 1.3 78.4 - - - +
99D ILE* 1.3 63.3 + - - +
125D ALA* 4.1 22.6 - - + +
128D ALA* 5.4 0.2 - - + -
129D ALA 5.3 0.4 - - - +
141D VAL* 4.2 11.7 - - + -
142D VAL 2.9 4.5 + - - +
143D PRO* 3.7 18.2 - - + -
144D HIS* 2.6 36.5 + - - +
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Residues in contact with ILE 99 (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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73D LEU* 3.6 34.3 - - + -
74D VAL 3.3 6.2 + - - +
75D ILE* 4.0 4.8 - - + +
76D GLY* 2.7 33.8 + - - -
98D VAL* 1.3 79.0 - - - +
100D ASP* 1.3 59.1 + - - +
144D HIS* 3.4 22.0 - - + +
146D ASN* 3.3 32.3 - - + +
147D LYS 4.3 2.0 - - - -
148D ILE* 4.0 22.9 - - + -
151D PHE* 4.0 11.0 - - + -
155D PHE* 3.7 20.2 - - + -
156D TYR* 4.2 9.9 - - + +
464J B39 4.2 2.8 + - + -
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Residues in contact with ASP 100 (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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77D ALA* 2.5 40.3 + - + +
98D VAL 4.2 0.4 - - - -
99D ILE* 1.3 76.0 - - - +
101D MET* 1.3 73.7 + - - +
102D ASP 2.9 16.2 + - - +
124D LYS* 3.5 15.1 - - - +
125D ALA* 4.2 14.0 + - + +
144D HIS 3.4 6.9 + - - +
145D PHE* 3.5 12.1 - - - -
146D ASN 3.3 17.5 + - - -
464J B39 2.7 39.3 + - - +
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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