Contacts of the strand formed by residues 33 - 44 (chain I) in PDB entry 3DXA
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 TYR 33 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150F ALA 4.8 1.6 + - - -
151F ARG* 4.0 14.0 + - - +
152F VAL* 5.6 0.3 - - - -
155F GLN* 3.5 37.1 - - + +
5H LEU* 4.4 9.1 - - + +
7H PHE* 4.1 22.8 - + - -
28I ILE* 4.4 0.3 - - - +
31I ASN 4.5 5.6 - - - -
32I GLU* 1.3 76.5 - - - +
39I VAL* 1.3 61.2 + - - +
40I TYR* 3.4 22.9 - + + -
55I HIS* 3.6 28.3 - + - -
56I GLY 4.0 2.7 - - - +
57I LEU* 3.6 41.2 - - + +
106I VAL* 3.5 6.9 - - - +
107I TRP* 2.7 50.1 + + - +
108I GLY 6.0 0.4 - - - -
109I GLY 5.2 2.2 - - - -
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Residues in contact with VAL 39 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I HIS* 3.9 22.4 - - + +
28I ILE* 3.8 22.0 - - + -
32I GLU 4.1 0.2 + - - -
33I TYR* 1.3 73.7 - - - +
40I TYR* 1.3 64.0 + - - +
41I TRP* 4.0 17.0 - - + +
55I HIS* 3.1 24.3 - - - +
56I GLY 3.0 15.2 + - - +
57I LEU 4.9 0.2 + - - -
58I LYS* 5.0 4.9 - - + -
81I LEU* 4.1 5.6 - - + +
83I ILE* 4.1 18.2 - - + -
87I SER* 3.6 24.0 - - - +
104I CYS* 4.7 5.6 - - - -
105I ILE 4.1 3.4 - - - +
106I VAL* 4.9 2.7 - - + +
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Residues in contact with TYR 40 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H PHE* 4.8 2.4 - - - -
33I TYR* 3.4 32.0 - - + -
39I VAL* 1.3 73.5 - - - +
41I TRP* 1.3 64.2 + - - +
42I TYR* 4.3 8.3 - + + -
52I TYR* 3.8 27.1 - + - -
54I ILE 3.9 1.3 - - - -
55I HIS* 3.6 21.9 - + + -
104I CYS* 3.7 2.8 - - - -
105I ILE* 2.8 54.8 + - + +
107I TRP* 3.7 32.3 - + + -
113J TYR* 3.5 9.5 - - - +
114J ASN* 2.8 52.6 + - + +
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Residues in contact with TRP 41 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLN* 3.6 22.7 - - - -
21I LEU* 3.2 32.8 - - + -
22I PRO 3.6 11.2 - - - -
23I CYS* 3.5 19.7 - - + -
39I VAL* 4.0 12.9 - - + +
40I TYR* 1.3 79.4 - - - +
42I TYR* 1.3 65.4 + - - +
52I TYR* 4.5 0.7 - - - -
53I ILE* 3.1 26.6 + - + +
54I ILE* 2.9 22.3 + - + +
81I LEU* 4.1 23.1 - - + +
87I SER* 3.9 17.3 + - - -
89I LEU* 3.3 45.2 - - + +
102I TYR* 4.2 17.3 - - + -
103I TYR 3.4 16.4 - - - -
104I CYS* 3.6 6.4 - - + -
119I THR* 5.5 1.1 - - - -
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Residues in contact with TYR 42 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I TYR* 4.3 9.2 + + - -
41I TRP* 1.3 81.1 - - - +
43I ARG* 1.3 58.8 + - - +
50I PRO* 3.9 14.6 - - + -
51I GLN 2.9 19.5 - - - -
52I TYR* 3.5 33.2 - + + -
53I ILE* 3.8 5.3 - - - +
102I TYR* 3.5 3.5 - - - +
103I TYR* 2.8 42.8 + - + +
105I ILE* 4.4 19.0 - - + +
113I VAL* 6.1 3.1 - - + -
115I PHE* 4.0 21.5 - + + -
114J ASN* 2.7 26.0 + - - -
115J GLU* 3.6 1.0 - - - -
116J GLN* 2.7 35.6 + - + +
118J PHE* 4.3 11.4 - + - -
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Residues in contact with ARG 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42I TYR* 1.3 72.7 - - - +
44I GLN* 1.3 62.6 + - - +
45I ILE* 3.9 27.1 + - + +
50I PRO* 3.4 2.7 - - - +
51I GLN* 2.9 56.8 + - + +
53I ILE* 3.3 24.2 - - + +
78I MET* 3.3 37.7 - - - +
91I LEU* 4.3 9.6 - - - +
97I ARG 5.3 0.4 + - - -
98I ASP* 3.7 26.8 + - - +
100I ALA* 4.1 7.0 - - + -
101I VAL 3.6 4.7 - - - -
102I TYR* 3.5 33.4 + - + -
103I TYR* 4.8 0.9 - - - -
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Residues in contact with GLN 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ARG* 1.3 71.7 - - - +
45I ILE* 1.3 57.6 + - - +
46I HIS 2.9 14.5 + - - +
48I GLN 3.6 7.5 - - - +
49I GLY* 3.6 30.9 - - - +
50I PRO* 3.8 15.9 - - + +
100I ALA* 3.8 2.7 - - - -
101I VAL* 2.8 34.5 + - + +
103I TYR* 2.7 46.3 + - + +
44J GLN* 3.1 37.4 + - - +
50J PRO* 4.1 3.4 - - - +
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Residues in contact with ILE 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43I ARG* 3.9 26.4 + - + +
44I GLN* 1.3 68.3 - - - +
46I HIS* 1.3 56.0 + - + +
47I SER 2.7 19.1 + - - -
48I GLN* 2.9 29.0 + - + +
49I GLY 4.9 3.6 - - - +
51I GLN* 3.3 28.5 - - - +
97I ARG 4.4 20.0 - - - +
99I THR 4.5 7.4 - - - +
100I ALA* 3.6 9.4 - - + -
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Residues in contact with HIS 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I GLN* 2.9 17.3 + - - +
45I ILE* 1.3 70.3 - - + +
47I SER* 1.3 89.1 + - - +
48I GLN 3.3 9.6 - - - +
99I THR 5.3 2.4 + - - +
100I ALA* 4.6 4.0 - - - +
101I VAL* 5.2 3.5 - - - +
187J PRO* 3.1 47.2 + - + +
188J GLN* 3.5 26.1 + - - -
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Residues in contact with SER 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I ILE 2.7 7.1 + - - -
46I HIS* 1.3 96.7 - - - +
48I GLN* 1.3 80.8 + - - +
101J MET* 6.0 2.1 - - - +
120J PRO 5.8 0.5 - - - +
169J GLU* 5.0 7.1 + - - -
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Residues in contact with GLN 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I GLN* 3.6 10.6 - - - +
45I ILE* 2.9 39.8 + - + +
46I HIS 3.3 10.6 - - - +
47I SER* 1.3 98.6 + - - +
49I GLY* 1.3 65.4 + - - +
44J GLN* 5.2 1.0 - - - +
103J LEU* 5.8 1.2 - - - +
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Residues in contact with GLY 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I GLN* 3.6 13.1 - - - +
45I ILE 4.9 2.4 - - - +
48I GLN* 1.3 83.5 - - - +
50I PRO* 1.3 80.3 - - - +
51I GLN* 3.6 0.9 + - - +
103J LEU* 5.0 13.0 - - - -
118J PHE* 4.3 8.7 - - - +
119J GLY 5.4 2.7 - - - -
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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