Contacts of the strand formed by residues 142 - 147 (chain P) 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 ARG 142 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25P TRP* 4.0 2.5 - - - -
32P PHE* 3.3 23.8 - - - -
34P ASN 5.3 0.2 + - - -
35P GLU* 2.7 52.9 + - - +
37P TYR* 3.8 10.6 + - - +
77P TYR* 3.1 57.5 + - + +
78P GLN* 3.4 24.9 + - - +
80P CYS* 5.2 0.2 - - - +
128P TYR 3.3 12.8 - - - +
129P ILE* 3.8 9.6 - - + -
140P CYS* 3.8 20.5 + - - +
141P LEU* 1.3 75.2 - - - +
143P LEU* 1.3 61.8 + - - +
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Residues in contact with LEU 143 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P VAL* 4.0 28.3 - - + -
25P TRP* 3.8 17.9 - - + -
32P PHE* 4.9 0.2 - - + -
37P TYR* 3.6 50.7 - - + +
38P THR 4.4 0.4 - - - +
39P ILE* 4.4 9.9 - - + -
47P VAL* 4.9 1.3 - - + -
49P ILE* 4.8 4.7 - - + -
77P TYR* 3.8 7.0 - - - -
127P TYR* 3.3 4.7 - - - -
128P TYR* 2.8 51.4 + - + +
142P ARG* 1.3 76.6 - - - +
144P LYS* 1.3 69.3 + - - +
145P VAL* 4.0 17.7 - - + -
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Residues in contact with LYS 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36L ASP* 4.3 5.7 + - - +
38L THR* 2.9 33.4 + - - +
77L TYR* 5.7 1.4 + - - -
144L LYS* 4.4 17.5 - - - +
37P TYR 3.1 8.1 + - - +
38P THR* 3.3 27.3 - - + +
39P ILE 3.0 24.8 + - - -
77P TYR* 4.0 12.7 - - + +
125P SER* 3.7 8.1 - - - -
126P TYR 3.4 4.7 - - - +
127P TYR* 3.5 34.4 + - + -
143P LEU* 1.3 74.2 - - - +
145P VAL* 1.3 66.2 + - - +
146P THR* 3.6 17.7 - - - +
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Residues in contact with VAL 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P ILE* 3.5 21.8 - - + -
41P VAL* 3.9 32.3 - - + -
47P VAL* 5.3 0.7 - - + -
108P PHE* 3.5 34.3 - - + -
125P SER* 3.2 2.6 - - - -
126P TYR* 2.7 38.3 + - + +
128P TYR* 3.9 28.7 - - + -
143P LEU* 4.0 9.0 - - + -
144P LYS* 1.3 77.5 - - - +
146P THR* 1.3 64.0 + - - +
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Residues in contact with THR 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L THR* 3.4 34.6 - - + +
39L ILE* 5.1 2.5 - - - -
40L HIS* 5.3 1.8 - - + +
38P THR* 4.3 5.8 - - - +
39P ILE 3.0 11.9 + - - -
40P HIS* 3.4 19.9 + - + +
41P VAL* 2.9 25.1 + - - +
123P GLY 5.9 0.2 - - - -
124P HIS 3.8 2.5 - - - +
125P SER* 2.9 21.8 + - - +
144P LYS* 3.6 17.3 - - - +
145P VAL* 1.3 74.7 - - - +
147P VAL* 1.3 68.5 + - - +
148P LYS* 5.2 0.9 - - - -
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Residues in contact with VAL 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L THR 5.4 0.2 - - - +
41P VAL* 3.5 7.4 - - + -
42P GLN 4.0 2.2 - - - -
43P LEU* 3.6 36.6 - - + +
108P PHE* 3.7 31.9 - - + -
120P PHE* 4.9 2.0 - - + -
121P LYS 3.4 17.9 - - - +
122P GLU* 3.8 5.4 - - - -
123P GLY* 2.7 28.1 + - - -
124P HIS 2.9 14.9 + - - +
126P TYR* 3.8 15.7 - - + -
145P VAL* 4.9 0.2 - - + -
146P THR* 1.3 78.6 - - - +
148P LYS* 1.3 68.9 + - - +
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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