Contacts of the strand formed by residues 71 - 78 (chain D) in PDB entry 2QJ9
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 THR 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D ILE* 4.3 12.7 - - - +
64D GLU 3.4 8.3 - - - -
65D GLU* 4.2 8.5 - - + +
69D GLY 4.6 3.4 - - - +
70D GLU* 1.3 83.0 - - - +
72D THR* 1.3 66.1 + - - +
115D LEU* 4.0 26.7 - - + +
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Residues in contact with THR 72 (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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62D ILE 3.9 0.5 - - - +
63D ILE* 3.4 8.6 - - - +
64D GLU* 2.8 49.1 + - - +
66D ASP* 4.3 10.5 + - + +
70D GLU* 3.7 21.2 + - + +
71D THR* 1.3 80.5 + - - +
73D LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 73 (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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41D SER* 4.3 8.9 + - - -
61D ALA* 5.2 2.9 - - + -
62D ILE 2.9 32.5 - - - +
63D ILE* 4.3 17.5 - - + -
72D THR* 1.3 83.0 - - - +
74D ALA* 1.3 71.2 + - - +
113D PRO* 5.0 11.7 - - + -
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Residues in contact with ALA 74 (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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41D SER* 3.3 17.5 - - - +
42D GLY* 4.6 4.3 - - - -
43D HIS* 3.5 24.0 - - + +
61D ALA* 3.4 1.7 - - - +
62D ILE* 2.8 42.8 + - + +
64D GLU* 5.0 5.4 - - - +
72D THR 4.3 0.2 - - - -
73D LEU* 1.3 80.2 - - - +
75D SER* 1.3 64.1 + - - +
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Residues in contact with SER 75 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D TYR* 3.8 4.9 + - - +
40D CYS* 3.5 6.2 - - - +
41D SER* 2.9 48.3 + - - +
43D HIS* 3.7 8.2 + - - +
60D PHE* 3.1 28.5 - - - -
61D ALA* 4.2 5.6 - - - -
74D ALA* 1.3 76.6 - - - +
76D GLY* 1.3 58.3 + - - +
108D ASN* 3.5 13.0 + - - -
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Residues in contact with GLY 76 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38D CYS* 4.0 0.7 - - - +
39D TYR 3.4 12.7 + - - -
40D CYS* 3.7 9.9 - - - -
43D HIS* 4.8 4.0 - - - -
53D CYS* 3.8 4.5 - - - -
59D CYS* 3.4 5.2 - - - -
60D PHE* 2.9 39.9 + - - -
75D SER* 1.3 78.3 - - - +
77D CYS* 1.3 59.9 + - - -
108D ASN* 3.7 3.6 + - - -
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Residues in contact with CYS 77 (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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52B ALA* 3.3 13.8 - - + +
53B ASP* 2.8 34.4 + - + -
54B HIS* 6.4 1.1 - - + -
38D CYS* 3.5 17.9 - - - -
43D HIS 5.4 1.2 + - - -
45D PRO* 6.3 0.2 - - + -
53D CYS* 2.1 64.1 - - + -
54D ILE 3.7 3.4 - - - +
55D THR* 3.7 18.2 - - - -
58D HIS 3.7 3.8 - - - -
60D PHE* 3.6 3.8 - - - -
76D GLY* 1.3 72.7 - - - -
78D MET* 1.3 57.4 + - - +
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Residues in contact with MET 78 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50B PRO* 4.2 5.6 - - + -
51B LEU 4.5 3.4 - - - +
52B ALA 4.8 0.4 - - - -
53B ASP 4.0 2.2 - - - +
55D THR* 3.0 8.4 + - - -
58D HIS* 2.8 46.1 + - + +
60D PHE* 3.9 14.6 - - + -
77D CYS* 1.3 75.7 - - - +
79D LYS* 1.3 69.3 + - - +
83D SER* 3.8 14.8 - - - -
86D GLN* 3.5 42.8 - - + +
87D CYS* 3.5 22.7 - - - -
99D ILE* 3.6 26.7 - - + -
101D CYS* 3.9 13.7 - - - -
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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