Contacts of the strand formed by residues 71 - 79 (chain b) in PDB entry 5EHD
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 PRO 71 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63b GLU* 4.5 21.4 - - + +
64b ALA* 3.3 13.7 - - - +
65b MET* 4.0 15.7 - - - -
69b GLY 4.4 0.7 - - - +
70b SER* 1.3 95.9 + - - +
72b ILE* 1.3 63.4 + - - +
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Residues in contact with ILE 72 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18a LEU* 3.4 30.8 - - + +
19a PHE* 3.9 1.1 - - + -
20a GLY* 3.7 26.7 - - - +
62b ALA 3.6 1.0 - - - +
63b GLU* 3.3 10.4 - - - -
64b ALA 2.8 33.8 + - - +
66b ASN* 3.0 37.5 - - + +
70b SER* 4.6 1.8 - - - +
71b PRO* 1.3 77.9 - - - +
73b LYS* 1.3 61.8 + - - +
74b VAL* 4.0 9.9 - - + -
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Residues in contact with LYS 73 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20a GLY* 5.1 4.2 - - - -
61b GLU* 3.1 37.0 + - + +
62b ALA 3.5 4.5 - - - -
63b GLU* 3.2 28.3 - - + +
72b ILE* 1.3 74.5 - - - +
74b VAL* 1.3 68.3 + - - +
101b ARG* 5.0 9.9 - - - +
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Residues in contact with VAL 74 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18a LEU* 3.9 24.7 - - + -
19a PHE 3.5 24.2 - - - +
20a GLY* 3.6 14.6 - - - +
112a SER* 3.3 29.2 - - - -
61b GLU* 3.1 7.2 - - - +
62b ALA 2.7 41.5 + - - +
72b ILE* 4.0 6.1 - - + -
73b LYS* 1.3 80.9 - - - +
75b THR* 1.3 66.4 + - - +
76b LEU* 3.6 12.0 + - + -
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Residues in contact with THR 75 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46a THR* 3.5 3.1 + - - -
48a SER* 3.5 20.3 + - - +
110a HIS* 3.3 45.1 + - + +
111a ILE 5.0 2.1 + - - -
112a SER* 3.1 23.3 + - - -
59b ILE* 3.6 28.4 - - + +
60b VAL 3.5 5.6 - - - +
61b GLU* 4.4 1.6 - - - +
74b VAL* 1.3 73.2 - - - +
76b LEU* 1.3 62.0 + - - +
77b ALA 3.9 6.7 - - - +
78b THR* 4.4 3.4 - - - +
103b LYS* 4.2 10.7 + - - +
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Residues in contact with LEU 76 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46a THR* 3.0 33.7 + - - +
48a SER* 4.5 1.1 - - - -
86a THR* 4.3 0.3 - - - +
44b LEU* 3.7 26.9 - - + -
47b VAL* 5.0 2.5 - - + -
60b VAL* 2.8 32.1 + - + +
62b ALA* 3.8 30.3 - - + +
74b VAL* 4.2 7.0 - - + -
75b THR* 1.3 77.2 - - - +
77b ALA* 1.3 62.3 + - + +
89b LEU* 4.0 14.2 - - + +
92b PHE* 3.6 35.0 - - + -
94b ILE* 4.9 1.8 - - + -
100b LEU* 3.9 10.5 - - + -
111b ILE* 5.0 3.4 - - + -
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Residues in contact with ALA 77 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48a SER* 4.3 1.6 - - - -
86a THR* 4.1 6.5 - - - -
47b VAL* 4.3 15.7 - - + -
58b HIS 3.8 0.7 - - - +
59b ILE* 3.4 4.7 - - - +
60b VAL* 2.9 29.7 + - + +
75b THR* 3.7 4.2 - - - +
76b LEU* 1.3 82.5 - - - +
78b THR* 1.3 62.5 + - - +
79b LEU* 3.9 20.0 - - + -
87b VAL* 4.1 25.6 - - + -
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Residues in contact with THR 78 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48a SER* 3.5 11.2 + - - -
49a LEU 3.0 26.6 + - - +
81a MET* 4.5 0.9 - - - -
85a PRO* 3.7 25.5 - - + +
86a THR* 2.7 31.6 + - - -
57b LEU* 3.6 34.3 - - + -
58b HIS 3.3 5.2 - - - +
59b ILE* 3.8 11.3 - - + +
75b THR* 4.4 3.6 - - - +
77b ALA* 1.3 74.6 + - - +
79b LEU* 1.3 68.3 + - - +
84b GLN* 4.0 1.7 + - - -
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Residues in contact with LEU 79 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85a PRO* 5.0 1.8 - - - -
47b VAL* 3.7 31.6 - - + +
49b LEU* 3.8 23.6 - - + -
56b GLU 3.7 1.0 - - - +
57b LEU* 3.7 5.1 - - - +
58b HIS* 2.8 39.6 + - + +
60b VAL* 4.4 6.3 - - + -
77b ALA* 3.9 13.7 - - + -
78b THR* 1.3 76.8 - - - +
80b LYS* 1.3 63.2 + - - +
84b GLN* 3.3 18.2 - - + +
85b PRO 3.9 10.5 - - - +
86b THR 4.0 0.9 - - - -
87b VAL* 3.3 44.0 - - + +
109b VAL* 5.0 1.8 - - + -
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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