Contacts of the strand formed by residues 104 - 109 (chain D) in PDB entry 4GAW
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 ILE 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D LEU* 4.0 18.8 - - + -
56D THR 3.4 8.1 - - - +
58D ALA* 3.3 3.9 - - - +
92D HIS* 2.8 45.3 + - + -
102D ASN 2.9 6.6 + - - +
103D ASP* 1.3 77.0 - - - +
105D MET* 1.3 64.4 + - - +
210D ILE* 3.9 24.9 - - + -
225D ILE* 4.0 22.9 - - + -
226D LYS 5.0 2.2 - - - +
227D VAL* 5.2 2.7 - - + -
230D PHE* 3.6 41.1 - - + -
233D TRP* 4.1 7.3 - - + -
234D ILE* 5.2 1.3 - - + -
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Residues in contact with MET 105 (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 VAL 3.5 1.7 - - - +
55D LEU* 3.5 5.7 - - - -
56D THR* 2.7 41.3 + - + +
57D ALA 3.3 23.3 - - - +
58D ALA* 3.4 15.0 - - - +
60D CYS 3.5 26.9 - - - +
61D GLN* 3.6 34.1 - - + +
65D ILE* 4.7 0.4 - - + -
89D PRO* 3.9 9.6 - - + -
91D PRO* 3.6 17.5 - - + -
104D ILE* 1.3 77.1 - - - +
106D LEU* 1.3 75.3 + - - +
107D LEU* 3.7 20.0 - - + -
233D TRP* 4.3 0.7 - - - -
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Residues in contact with LEU 106 (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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49D VAL* 5.0 2.5 - - + -
53D PHE* 4.2 22.0 - - + -
54D VAL 4.1 7.9 - - - +
55D LEU* 3.7 22.4 - - + -
89D PRO 3.8 0.2 - - - -
90D ILE* 2.7 53.5 + - + +
105D MET* 1.3 75.1 - - - +
107D LEU* 1.3 58.1 + - - +
108D GLN 4.0 0.4 - - - -
233D TRP* 3.7 15.0 - - + -
234D ILE* 3.8 27.8 - - + +
237D THR* 3.5 36.6 - - + +
238D MET* 4.0 12.6 - - + -
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Residues in contact with LEU 107 (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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33D VAL* 4.1 19.5 - - + -
53D PHE* 3.3 10.4 - - - -
54D VAL* 2.7 41.5 + - + +
56D THR* 3.9 18.4 - - + -
65D ILE* 4.4 11.4 - - + -
67D VAL* 3.8 28.7 - - + -
86D VAL* 4.1 19.7 - - + -
88D ARG 4.2 0.7 - - - -
89D PRO* 4.3 13.7 - - + -
105D MET* 3.7 31.4 - - + -
106D LEU* 1.3 71.6 - - - +
108D GLN* 1.3 61.7 + - - +
109D LEU* 3.6 3.1 + - + +
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Residues in contact with GLN 108 (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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52D ASP* 3.6 7.0 - - + +
53D PHE* 3.8 26.5 - - + -
86D VAL* 3.6 3.4 - - - +
87D LYS* 2.8 70.4 + - - +
88D ARG* 3.1 57.6 + - + +
90D ILE* 4.0 3.1 - - + +
106D LEU 4.0 1.0 - - - -
107D LEU* 1.3 71.2 - - - +
109D LEU* 1.3 66.0 + - - +
241D LEU* 3.3 28.7 - - + +
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Residues in contact with LEU 109 (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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48D LEU* 4.4 5.8 - - + -
51D LYS 4.1 15.7 - - - +
52D ASP* 2.7 34.8 + - - +
53D PHE 4.1 0.2 - - - +
54D VAL* 4.2 14.6 - - + -
67D VAL* 4.2 9.9 - - + -
69D LEU* 4.2 14.4 - - + -
84D ILE* 3.8 34.3 - - + -
85D PRO 3.9 5.6 - - - +
86D VAL* 3.9 21.1 - - + +
87D LYS* 3.5 13.7 + - - +
107D LEU* 4.0 10.8 - - + +
108D GLN* 1.3 83.0 + - - +
110D GLU* 1.3 64.4 + - - +
111D ARG 3.6 7.4 - - - +
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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