Contacts of the strand formed by residues 64 - 73 (chain I) in PDB entry 4XLN
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 LEU 64 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54I ILE 3.6 1.3 - - - +
55I GLU* 3.3 29.6 + - - +
56I GLU 3.8 5.9 + - - -
63I GLY* 1.3 75.3 - - - +
65I VAL* 1.3 65.7 + - - +
66I LEU* 4.3 1.6 - - + +
100I LEU* 3.6 38.4 - - + -
101I ILE 3.3 33.9 - - - +
102I HIS* 3.7 18.4 - - + +
103I LYS* 4.7 4.6 - - - +
359I MET* 3.6 42.7 - - + +
372I LEU* 3.9 8.3 - - + -
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Residues in contact with VAL 65 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I PRO* 3.9 26.7 - - + -
54I ILE 3.4 4.0 - - - +
55I GLU* 4.1 15.0 - - + -
64I LEU* 1.3 76.2 - - - +
66I LEU* 1.3 63.7 + - - +
67I ASP* 4.9 6.7 - - + +
101I ILE* 2.9 64.8 + - + +
103I LYS* 4.7 16.4 - - + +
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Residues in contact with LEU 66 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I PHE* 3.2 15.3 - - + -
53I PRO* 3.3 3.7 - - - +
54I ILE* 2.9 47.3 + - + +
64I LEU* 4.3 3.3 - - + +
65I VAL* 1.3 72.5 - - - +
67I ASP* 1.3 59.5 + - - +
98I LEU* 3.6 35.2 - - + -
99I GLN 3.3 21.5 - - - +
100I LEU* 3.8 9.4 - - + +
355I VAL* 4.0 23.3 - - + -
359I MET* 5.7 0.2 - - - -
369I PRO* 4.3 3.6 - - + -
372I LEU* 3.7 35.2 - - + -
373I VAL* 5.1 2.0 - - + -
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Residues in contact with ASP 67 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I PHE* 3.5 7.0 - - - +
53I PRO* 3.8 24.7 - - + +
65I VAL* 3.9 6.7 + - + +
66I LEU* 1.3 71.8 - - - +
68I PHE* 1.3 77.3 + - - +
98I LEU* 3.2 7.8 - - - +
99I GLN* 2.9 60.3 + - + +
101I ILE* 4.8 4.0 - - + -
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Residues in contact with PHE 68 (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 GLN* 3.9 24.2 - - + -
48I PHE* 3.5 53.6 - + + -
49I LYS* 4.8 11.2 - - + -
52I PHE* 3.3 38.8 - + + -
67I ASP* 1.3 89.0 + - - +
69I LEU* 1.3 82.7 + - - +
70I GLU* 3.6 33.7 - - - -
71I TYR 4.4 0.4 - - - -
96I ALA* 5.9 1.1 - - + -
97I ARG 4.1 5.4 - - - -
98I LEU* 5.5 0.4 - - + -
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Residues in contact with LEU 69 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I PRO 4.9 4.7 - - - +
45I GLN* 5.3 0.3 - - - +
68I PHE* 1.3 97.9 - - - +
70I GLU* 1.3 70.4 + - + +
97I ARG* 2.9 36.8 + - + +
98I LEU* 3.6 19.1 - - - +
99I GLN* 3.6 25.1 - - + +
110I GLU* 3.3 34.5 - - - +
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Residues in contact with GLU 70 (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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36I PRO* 3.2 41.3 - - + +
39I ARG* 3.8 4.9 - - - +
45I GLN* 4.9 0.9 - - - +
68I PHE* 3.6 19.8 - - - -
69I LEU* 1.3 86.5 - - - +
71I TYR* 1.3 62.3 + - - +
96I ALA* 3.7 0.5 - - - -
97I ARG* 2.6 57.5 + - + +
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Residues in contact with TYR 71 (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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30I LEU 2.5 29.5 + - - -
31I GLN* 3.4 14.1 + - - +
36I PRO* 5.7 0.2 - - - +
39I ARG* 3.0 51.8 + - - -
44I ILE* 3.2 23.9 - - + +
45I GLN* 3.1 31.1 + - - -
48I PHE* 3.7 33.7 - + + -
68I PHE* 4.5 0.4 - + - -
70I GLU* 1.3 80.5 - - - +
72I ARG* 1.3 59.0 + - - +
73I ILE* 3.9 15.7 - - + -
94I LEU* 3.7 24.7 - - + -
95I TYR 3.5 8.1 - - - +
96I ALA* 4.3 2.7 - - - +
97I ARG* 4.3 0.4 - - - +
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Residues in contact with ARG 72 (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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71I TYR* 1.3 72.5 - - - +
73I ILE* 1.3 76.7 + - + +
74I GLY* 3.6 3.9 + - - -
75I ASP* 3.8 22.4 + - - -
94I LEU* 3.2 11.2 - - - +
95I TYR* 2.5 86.4 + - + +
112I GLU* 4.6 9.4 + - - +
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Residues in contact with ILE 73 (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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30I LEU* 5.0 3.4 - - + +
32I ALA* 3.3 55.4 - - + +
33I ASP* 4.6 5.8 - - - +
39I ARG* 5.0 4.2 - - - +
71I TYR* 3.9 24.3 + - + -
72I ARG* 1.3 80.7 + - + +
74I GLY* 1.3 66.4 + - - +
75I ASP* 3.9 4.3 + - - +
94I LEU* 4.5 7.6 - - + -
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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
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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