Contacts of the strand formed by residues 97 - 103 (chain A) in PDB entry 6X34
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 4.6 2.7 - - - -
30A LEU* 5.3 0.2 - - - -
36A PHE* 4.8 8.5 - - + -
76A CYS* 3.5 34.8 + - + +
77A THR 5.5 1.4 + - - +
81A ALA* 4.8 16.4 - - + +
91A ILE* 5.6 7.6 - - + -
95A ALA 5.3 0.2 - - - +
96A THR* 1.3 80.2 - - - +
98A ILE* 1.3 63.5 + - - +
99A PHE* 3.6 25.8 - - + -
1785B ALA* 6.0 2.7 - - + -
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Residues in contact with ILE 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 3.9 0.3 - - - +
28A GLY* 3.3 4.0 - - - -
29A MET* 2.9 56.9 + - + +
30A LEU* 4.6 10.3 - - - -
31A GLN* 4.8 2.9 - - + +
36A PHE* 4.5 1.1 - - - -
73A LYS* 4.6 17.9 - - + -
74A LEU 4.1 7.9 - - - +
75A THR* 4.4 26.0 - - + +
96A THR* 3.7 23.1 - - - +
97A LEU* 1.3 74.1 - - - +
99A PHE* 1.3 64.5 + - - +
100A ASP* 5.0 2.2 - - + +
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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* 4.1 22.7 - + + -
27A THR 3.4 2.0 - - - +
28A GLY* 4.2 6.3 - - - -
36A PHE* 3.7 27.6 - + - -
37A ASP* 3.8 8.5 - - - -
59A PHE* 4.3 32.1 - + + -
74A LEU* 2.8 43.3 + - + +
76A CYS* 3.5 23.8 - - + -
81A ALA* 5.0 7.9 - - + -
97A LEU* 3.6 31.2 - - + -
98A ILE* 1.3 75.9 - - - +
100A ASP* 1.3 56.6 + - - +
101A VAL* 3.1 5.2 + - + +
1784B VAL 4.8 8.7 - - - -
1785B ALA* 4.7 16.4 - - + -
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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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25A HIS 4.0 2.1 - - - +
26A TYR* 3.5 3.7 - - - -
27A THR* 2.7 39.8 + - - +
71A ARG* 5.7 1.5 - - + +
72A ALA 3.6 9.6 - - - +
73A LYS* 4.2 11.7 - - + +
98A ILE* 4.1 2.3 - - + +
99A PHE* 1.3 68.0 - - - +
101A VAL* 1.3 64.3 + - - +
102A GLU* 3.6 2.3 + - - +
674B PHE* 5.8 3.3 - - + -
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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* 4.4 9.6 - - + -
26A TYR* 4.1 7.4 - - + -
48A PHE* 6.5 0.2 - - + -
59A PHE* 4.2 31.4 - - + +
62A GLY 4.8 12.3 - - - +
63A ALA* 4.9 13.0 - - + -
66A MET* 5.2 7.4 - - + -
70A GLN 4.2 0.7 - - - +
71A ARG* 3.3 2.1 - - - +
72A ALA* 3.0 41.4 + - + +
74A LEU* 4.0 19.1 - - + -
99A PHE 3.1 3.3 + - - +
100A ASP* 1.3 74.0 - - - +
102A GLU* 1.3 61.3 + - - +
103A LEU* 4.1 14.5 + - + +
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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 13.0 - - - +
25A HIS* 3.4 28.0 + - + +
70A GLN 3.9 6.3 - - - -
71A ARG* 3.8 17.7 - - + +
100A ASP 3.6 3.2 + - - +
101A VAL* 1.3 73.9 - - - +
103A LEU* 1.3 65.6 + - - +
104A LEU* 3.3 6.8 + - - +
674B PHE* 4.0 20.9 - - + -
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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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14A THR 5.9 0.9 - - - +
16A PRO* 4.2 15.5 - - + -
22A CYS* 5.0 10.8 - - + -
23A VAL 4.7 1.8 - - - +
24A VAL* 3.7 10.5 - - + +
63A ALA* 4.0 18.2 - - + +
66A MET* 3.9 25.3 - - + +
67A SER 3.3 24.7 - - - +
68A LEU* 3.7 14.1 - - + +
69A GLY* 3.1 25.8 + - - -
70A GLN 3.4 11.2 + - - +
101A VAL* 3.9 5.5 - - + +
102A GLU* 1.3 71.9 - - - +
104A LEU* 1.3 59.4 + - - +
105A ASN* 3.5 29.8 - - + +
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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