Contacts of the strand formed by residues 109 - 116 (chain D) in PDB entry 3VI4
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 109 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D GLY* 3.8 9.3 + - - -
66D SER* 3.7 29.4 - - - +
67D LYS* 3.9 8.7 + - - +
101D LEU* 3.8 20.7 - - + +
102D ARG 3.6 20.6 - - - +
103D LEU* 3.8 17.4 - - + +
107D GLU* 3.8 25.0 + - - +
108D PRO* 1.3 88.8 + - - +
110D THR* 1.3 63.7 + - - +
111D PHE* 4.9 0.2 - - - -
409D SER* 3.3 1.0 - - - -
410D ILE* 3.0 33.0 + - - +
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Residues in contact with THR 110 (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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67D LYS* 3.3 23.4 + - - +
101D LEU* 5.1 0.4 - - - +
108D PRO* 4.3 9.2 + - + +
109D GLN* 1.3 77.8 + - - +
111D PHE* 1.3 62.7 + - - +
407D GLU* 5.0 12.4 - - + +
408D ILE 3.2 8.7 - - - -
409D SER* 2.9 27.6 - - - -
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Residues in contact with PHE 111 (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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67D LYS* 3.1 24.7 - - + +
69D ILE* 6.2 0.2 - - + -
96D PRO* 5.5 2.2 - - + -
99D LEU* 3.6 27.1 - - + -
101D LEU* 3.7 31.4 - - + -
109D GLN 5.3 0.2 - - - -
110D THR* 1.3 75.4 - - - +
112D THR* 1.3 67.2 + - - +
113D LEU* 3.6 31.2 - - + -
406D PHE 3.7 0.3 - - - +
407D GLU* 3.8 1.3 - - - -
408D ILE* 2.9 70.4 + - + +
410D ILE* 4.0 7.4 - - + -
425D ILE* 3.8 6.7 - - + -
436D VAL* 3.8 21.5 - - + -
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Residues in contact with THR 112 (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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67D LYS* 3.6 11.0 + - - +
95D GLN 4.1 0.2 - - - +
96D PRO* 3.5 19.9 - - - +
111D PHE* 1.3 81.3 - - - +
113D LEU* 1.3 63.3 + - - +
114D LYS* 5.6 5.0 - - - +
405D GLN* 4.5 15.4 + - - +
406D PHE 3.1 9.6 - - - -
407D GLU* 3.5 33.2 - - + +
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Residues in contact with LEU 113 (chain D).
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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94D ILE* 5.1 9.4 - - + -
95D GLN 3.3 8.3 - - - +
96D PRO* 4.1 11.2 - - + -
111D PHE* 3.6 31.2 - - + -
112D THR* 1.3 73.7 - - - +
114D LYS* 1.3 63.0 + - - +
115D PHE 4.2 0.2 + - - -
364D LEU* 4.0 20.2 - - + -
405D GLN* 3.2 8.0 - - - +
406D PHE* 2.7 44.1 + - + +
408D ILE* 3.9 17.5 - - + -
425D ILE* 4.1 7.9 - - + -
427D PRO* 6.5 0.2 - - + -
434D VAL* 3.9 35.7 - - + -
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Residues in contact with LYS 114 (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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75D VAL* 4.3 6.3 - - + +
93D GLN 3.4 0.9 - - - +
94D ILE* 3.3 7.4 - - - +
95D GLN* 2.7 64.9 + - + +
112D THR* 5.6 5.2 - - - +
113D LEU* 1.3 76.1 - - - +
115D PHE* 1.3 61.8 - - - +
116D LYS 4.2 0.2 + - - -
403D GLU* 4.3 18.1 + - + +
404D VAL 3.4 3.6 - - - +
405D GLN* 3.4 35.0 - - + +
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Residues in contact with PHE 115 (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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93D GLN* 3.2 42.0 - - + -
94D ILE* 3.6 17.9 - - + -
113D LEU 4.2 0.2 - - - -
114D LYS* 1.3 75.6 - - - +
116D LYS* 1.3 59.1 + - - +
117D ARG* 3.6 26.0 - - + -
362D VAL* 3.2 36.3 - - + -
364D LEU* 5.8 0.9 - - + -
398D ILE* 4.4 12.3 - - + -
402D ASP 3.7 0.5 - - - +
403D GLU* 3.3 5.2 - - - +
404D VAL* 2.7 44.0 + - + +
406D PHE* 4.2 19.5 - - + -
427D PRO* 4.1 22.0 - - + -
430D PHE* 3.9 19.5 - + - -
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Residues in contact with LYS 116 (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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75D VAL* 3.0 37.9 - - + +
76D THR 3.6 16.2 - - - +
77D ASN* 4.9 8.3 - - - +
78D ARG* 4.9 12.2 - - - +
92D HIS 4.3 1.2 - - - +
93D GLN* 2.8 34.5 + - - +
114D LYS 4.2 0.2 - - - -
115D PHE* 1.3 78.4 - - - +
117D ARG* 1.3 68.0 + - - +
118D ALA* 3.5 1.4 + - - +
401D GLY* 3.1 34.1 + - - +
402D ASP 3.4 3.1 - - - -
403D GLU* 3.3 29.7 + - + +
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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