Contacts of the strand formed by residues 97 - 106 (chain A) in PDB entry 1D7I
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A MET 3.7 4.0 - - - +
30A LEU* 3.7 30.5 - - + -
36A PHE* 3.8 17.0 - - + -
56A ILE* 4.9 0.2 - - + -
74A LEU 3.7 0.9 - - - +
75A THR* 3.6 2.1 - - - -
76A ILE* 2.8 41.0 + - + +
81A ALA* 3.8 15.3 - - + -
82A TYR* 3.7 35.4 - - + -
91A ILE* 4.3 5.6 - - + -
95A ALA* 3.8 17.7 + - + +
96A THR* 1.3 79.8 - - - +
98A VAL* 1.3 62.6 + - - +
99A PHE* 3.6 28.5 - - + -
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR 3.7 1.4 - - - +
28A GLY* 3.7 1.0 - - - -
29A MET* 2.8 60.4 + - + +
30A LEU 5.1 6.1 - - - +
31A GLU* 5.2 6.1 - - - -
73A LYS* 3.7 29.6 - - + -
74A LEU 3.2 9.2 - - - +
75A THR* 4.2 17.0 - - + +
96A THR* 5.0 6.3 - - + +
97A LEU* 1.3 76.8 - - - +
99A PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 4.2 10.8 - + + -
27A THR 3.3 4.7 - - - -
28A GLY* 3.7 22.9 - - - -
29A MET* 4.8 0.2 - - - -
36A PHE* 3.7 22.0 - + - -
56A ILE* 4.2 4.0 - - + -
59A TRP* 3.5 34.5 - + - +
72A ALA 3.7 0.7 - - - +
73A LYS* 3.2 6.8 - - - +
74A LEU* 2.7 42.2 + - + +
76A ILE* 3.7 19.1 - - + -
97A LEU* 3.6 30.5 - - + -
98A VAL* 1.3 79.1 - - - +
100A ASP* 1.3 60.2 + - - +
101A VAL* 3.6 17.0 + - + -
301A DSS 3.7 26.2 - - + -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.0 13.5 - - + +
25A HIS 3.8 0.5 - - - +
26A TYR* 3.0 24.4 - - - -
27A THR* 3.0 19.7 + - - +
29A MET* 4.1 16.2 - - + +
40A ARG* 4.7 5.8 + - - -
71A ARG* 2.9 47.7 + - - +
72A ALA 3.6 3.6 - - - -
73A LYS* 4.6 3.4 - - + +
99A PHE* 1.3 70.1 - - - +
101A VAL* 1.3 59.8 + - - +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.2 19.3 - - + -
25A HIS 3.4 8.3 - - - +
26A TYR* 4.1 10.1 - - + -
59A TRP* 4.2 9.6 - - + -
63A VAL* 4.4 9.4 - - + -
66A MET* 3.3 22.7 - - + +
71A ARG* 3.3 1.0 - - - -
72A ALA 2.8 39.7 + - - +
74A LEU* 3.9 19.1 - - + -
99A PHE* 3.7 23.6 - - + +
100A ASP* 1.3 79.7 - - - +
102A GLU* 1.3 67.0 + - - +
103A LEU* 4.6 0.4 - - - +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.3 6.9 - - - -
25A HIS* 2.9 31.4 + - + +
40A ARG* 3.1 32.3 + - - +
69A GLY* 4.5 8.0 - - - +
70A GLN 3.4 11.0 - - - +
71A ARG* 3.5 27.7 + - + +
100A ASP 4.3 0.2 + - - -
101A VAL* 1.3 75.4 - - - +
103A LEU* 1.3 62.4 + - - +
104A LEU* 3.0 28.7 + - + +
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Residues in contact with LEU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PRO* 3.8 25.8 - - + -
22A CYS* 4.0 14.8 - - + -
23A VAL 3.9 1.3 - - - +
24A VAL* 3.7 23.1 - - + -
63A VAL* 4.5 6.7 - - + +
66A MET* 4.0 22.6 - - + +
67A SER 3.7 27.8 - - - +
68A VAL* 3.9 7.6 - - + +
69A GLY* 2.7 35.0 + - - -
70A GLN 2.9 14.8 + - - +
102A GLU* 1.3 69.5 - - - +
104A LEU* 1.3 57.9 + - - +
105A LYS 3.8 19.7 - - - +
106A LEU* 4.1 7.4 - - + -
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 2.9 22.6 + - + +
24A VAL* 4.6 3.1 - - - -
25A HIS* 4.5 16.4 - - + +
45A PRO* 3.9 34.1 - - + -
68A VAL* 4.0 8.8 - - - +
69A GLY* 5.0 2.1 + - - -
102A GLU* 3.0 38.3 + - - +
103A LEU* 1.3 73.4 - - - +
105A LYS* 1.3 68.0 + - + +
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Residues in contact with LYS 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 3.2 46.6 + - + +
68A VAL* 4.0 14.1 - - + +
103A LEU* 3.6 4.7 - - - +
104A LEU* 1.3 82.6 - - + +
106A LEU* 1.3 74.0 + - - +
107A GLU* 3.1 36.6 + - - +
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Residues in contact with LEU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A THR* 4.2 23.6 - - + -
15A PHE 4.3 0.4 - - - +
16A PRO* 3.9 34.1 - - + -
20A GLN* 3.4 39.5 - - + +
21A THR 3.3 4.0 - - - +
22A CYS* 4.0 19.5 - - - -
68A VAL* 4.0 12.9 - - + +
103A LEU* 4.1 8.7 - - + -
105A LYS* 1.3 89.4 - - - +
107A GLU* 1.3 67.2 + - - +
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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