Contacts of the strand formed by residues 67 - 72 (chain D) in PDB entry 3HEI
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 TYR 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D TRP* 3.8 20.0 - + - -
27D SER* 4.0 4.5 + - - -
52D PRO* 3.8 24.7 - - + -
65D GLU* 2.7 42.8 + - + +
66D GLN* 1.3 80.2 - - - +
68D ILE* 1.3 60.5 + - - +
69D LEU* 4.0 6.2 + - + -
91D GLN* 3.7 1.7 - - - -
92D CYS* 2.7 45.5 + - + +
130D SER* 3.7 23.3 - - - -
131D LYS 3.3 14.6 - - - +
132D PRO* 3.7 18.2 - - + -
133D ILE* 3.8 11.0 - - - +
135D GLN* 4.9 2.8 + - - -
141D LEU* 3.4 27.0 - - + +
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Residues in contact with ILE 68 (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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67D TYR* 1.3 74.4 - - - +
69D LEU* 1.3 62.3 + - - +
70D TYR* 3.5 38.3 - - + +
85D LYS* 5.8 1.8 - - - +
88D VAL* 3.8 28.5 - - + -
90D TRP 3.9 3.1 - - - +
91D GLN* 3.5 25.6 - - + +
130D SER* 3.1 6.9 - - - -
131D LYS* 2.9 40.8 + - + +
132D PRO 5.3 1.1 - - - +
133D ILE* 4.1 14.8 - - + -
34O ASP* 3.8 29.8 - - + +
85P LYS* 4.7 7.0 - - - +
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Residues in contact with LEU 69 (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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25D TRP* 3.8 40.4 - - + +
49D ILE* 3.7 35.4 - - + -
67D TYR* 4.2 7.6 - - + -
68D ILE* 1.3 73.2 - - - +
70D TYR* 1.3 62.2 + - - +
88D VAL* 3.7 5.2 - - - +
89D ARG* 2.7 27.5 + - + -
90D TRP* 2.8 28.0 + - + +
92D CYS* 3.9 22.7 - - - +
104D LEU* 4.5 15.0 - - + -
128D TYR* 5.4 4.9 - - + -
129D ILE 3.6 2.7 - - - +
130D SER* 3.9 9.9 - - - -
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Residues in contact with TYR 70 (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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68D ILE* 3.5 42.7 - - + +
69D LEU* 1.3 76.3 - - - +
71D LEU* 1.4 59.9 + - - +
72D VAL* 3.6 17.7 + - + -
82D PRO* 3.6 31.6 - - + -
84D SER 4.5 4.7 - - - -
85D LYS* 5.2 4.4 - - + +
87D GLN* 3.3 9.2 - - + +
88D VAL* 3.7 36.8 - - + +
89D ARG* 4.1 2.9 - - - -
127D TYR 3.9 0.2 - - - +
128D TYR* 3.1 10.3 - - - +
129D ILE* 2.8 52.1 + - + +
130D SER* 4.5 0.4 - - - -
131D LYS* 3.8 20.6 - - + +
33O ASN* 4.2 15.1 + - + +
34O ASP* 4.8 2.6 + - - -
35O MET* 4.3 2.9 - - - +
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Residues in contact with LEU 71 (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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70D TYR* 1.4 70.6 - - - +
72D VAL* 1.4 61.8 + - - +
87D GLN* 3.0 28.0 + - - +
89D ARG* 3.9 24.1 - - + +
106D GLU* 4.1 16.4 - - - +
118D LYS* 3.7 39.5 - - + +
120D PHE* 4.4 3.1 - - + -
126D TYR* 4.6 10.8 - - + -
127D TYR 3.4 24.5 - - - +
128D TYR* 3.9 24.9 - - + +
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Residues in contact with VAL 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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70D TYR* 3.6 24.2 - - + -
71D LEU* 1.4 81.6 - - - +
73D GLU* 1.3 78.4 + - - +
76D GLU* 3.6 12.1 - - + -
77D TYR 3.7 14.4 - - - +
82D PRO* 4.3 2.2 - - + -
87D GLN* 3.7 24.2 - - - +
126D TYR* 5.3 0.2 - - - -
127D TYR* 2.9 41.6 + - + +
129D ILE* 4.1 26.0 - - + +
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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