Contacts of the helix formed by residues 71 - 80 (chain D) in PDB entry 3ZNG
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 SER 71 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41D HIS* 3.6 4.3 - - - -
62D VAL 4.9 4.0 - - - -
63D ASN* 5.5 3.1 - - - -
64D ILE 3.4 10.1 - - - -
65D ILE* 4.6 7.2 - - - -
69D HIS 3.8 0.8 + - - -
70D VAL* 1.3 77.3 - - - +
72D PRO* 1.3 76.2 - - - +
73D LEU* 3.5 11.8 + - - +
74D HIS* 2.9 47.8 + - - +
75D GLU* 3.2 8.1 + - - +
94D GLN 4.9 5.1 + - - -
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Residues in contact with PRO 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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40D MET* 3.6 23.6 - - + +
41D HIS* 3.5 21.1 - - + +
44D ALA* 3.2 25.4 - - + +
62D VAL 3.7 9.9 - - - +
64D ILE* 3.3 34.5 - - + +
71D SER* 1.3 85.3 - - - +
73D LEU* 1.3 56.9 + - - +
75D GLU* 3.0 3.5 + - + +
76D ALA* 2.8 26.7 + - - +
88D LEU* 3.8 15.5 - - + -
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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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62D VAL* 5.4 1.2 + - - +
71D SER* 3.1 10.1 + - - +
72D PRO* 1.3 77.5 - - - +
74D HIS* 1.3 62.5 + - - +
76D ALA* 3.8 0.6 - - - +
77D CYS* 3.0 45.3 + - - -
85D VAL* 4.1 28.5 - - + +
88D LEU* 3.8 14.0 - - + +
89D LEU* 3.9 14.1 - - + -
93D ALA* 3.7 25.6 - - + -
94D GLN 3.4 29.8 - - - +
95D VAL* 3.9 10.5 - - + -
105D PRO* 4.0 13.5 - - + -
121D LEU* 4.5 2.2 - - + -
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Residues in contact with HIS 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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69D HIS 3.8 17.5 - - - -
70D VAL* 3.7 12.9 - - + -
71D SER* 2.9 41.0 + - - +
73D LEU* 1.3 77.9 - - - +
75D GLU* 1.3 64.0 + - - +
77D CYS* 3.9 0.7 - - - +
78D LEU* 3.1 19.6 + - - +
94D GLN 5.5 0.9 - - - -
97D GLY* 3.0 38.1 + - - -
99D THR* 3.7 15.7 - - + -
103D HIS 3.4 5.8 + - - -
104D THR 3.7 5.4 - - - -
105D PRO* 3.3 31.3 - - + +
108D ASN* 3.2 24.4 + - - +
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Residues in contact with GLU 75 (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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37D TRP* 3.2 26.0 - - - -
41D HIS* 4.1 11.7 - - + +
44D ALA* 3.8 7.9 - - + +
45D ILE* 3.6 40.5 - - + +
70D VAL* 3.7 20.7 - - + +
71D SER 3.6 12.6 - - - +
72D PRO* 3.0 6.8 + - + +
74D HIS* 1.3 75.3 - - - +
76D ALA* 1.3 65.2 + - - +
78D LEU* 3.5 20.0 + - - +
79D GLY* 3.3 17.0 + - - -
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Residues in contact with ALA 76 (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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44D ALA* 3.5 13.8 + - + +
72D PRO 2.8 18.7 + - - +
73D LEU* 3.8 4.0 - - - +
75D GLU* 1.3 73.2 - - - +
77D CYS* 1.3 63.3 + - - +
79D GLY* 3.2 3.3 + - - -
80D GLY 3.2 3.5 + - - -
81D HIS* 3.1 26.1 + - - +
84D CYS* 3.9 24.2 - - + -
85D VAL* 3.9 17.7 - - + -
88D LEU* 4.0 12.3 - - + -
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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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73D LEU* 3.0 43.4 + - - +
74D HIS 3.9 3.4 - - - +
76D ALA* 1.3 73.8 - - - +
78D LEU* 1.3 66.2 + - - +
80D GLY* 3.2 11.2 + - - +
85D VAL* 3.8 14.1 - - - -
105D PRO* 3.4 25.8 - - + +
108D ASN* 3.6 6.6 - - + +
109D ALA* 3.6 9.8 - - + +
112D SER* 3.4 14.6 + - - -
117D CYS* 5.1 3.0 - - - -
121D LEU* 3.7 26.9 - - - -
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Residues in contact with LEU 78 (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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74D HIS 3.1 16.6 + - - +
75D GLU* 3.6 20.4 - - - +
76D ALA 3.3 0.4 - - - -
77D CYS* 1.3 78.4 - - - +
79D GLY* 1.3 55.3 + - - +
108D ASN* 3.8 35.6 - - + +
111D VAL* 4.1 22.3 - - + +
112D SER* 3.3 18.0 - - - -
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Residues in contact with GLY 79 (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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45D ILE 5.0 2.0 - - - -
75D GLU 3.3 4.9 + - - -
76D ALA 3.2 3.8 + - - -
77D CYS 3.2 0.6 - - - -
78D LEU* 1.3 79.6 - - - +
80D GLY* 1.3 63.4 + - - +
81D HIS* 3.2 33.5 - - - -
112D SER* 4.3 2.2 - - - -
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Residues in contact with GLY 80 (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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76D ALA 3.2 0.4 + - - -
77D CYS 3.2 15.9 + - - -
78D LEU 3.4 0.6 + - - -
79D GLY* 1.3 79.0 - - - +
81D HIS* 1.3 60.5 + - - +
82D LEU* 3.1 8.9 + - - +
112D SER* 3.8 4.9 - - - -
114D SER* 3.9 25.8 + - - -
117D CYS* 3.9 8.0 - - - -
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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