Contacts of the strand formed by residues 71 - 77 (chain Q) in PDB entry 5HJD
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 71 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35Q PHE* 3.3 7.6 - - - +
36Q VAL* 3.1 48.0 + - + +
44Q ILE* 4.0 26.2 - - + -
45Q GLN* 3.5 29.1 - - - +
48Q VAL* 3.7 24.6 + - + +
49Q GLU 5.5 0.2 + - - -
50Q LYS* 4.8 1.6 - - - -
51Q VAL* 3.5 41.5 - - + -
53Q PHE* 3.7 7.0 - - - -
66Q CYS* 3.8 26.0 - - + -
67Q LYS 4.4 3.4 + - - -
68Q ASP* 3.9 17.7 - - - -
69Q PRO* 4.0 16.7 - - + +
70Q PRO* 1.3 67.7 - - - +
72Q LYS* 1.3 57.6 + - - +
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Residues in contact with LYS 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Q MET* 3.5 39.8 - - + +
34Q VAL 3.6 3.4 - - - +
35Q PHE* 4.8 6.1 - - + +
53Q PHE* 4.5 0.2 - - - -
66Q CYS* 3.4 16.7 - - - -
70Q PRO* 3.0 44.1 + - + +
71Q TYR* 1.3 74.1 - - - +
73Q VAL* 1.3 69.3 + - - +
74Q GLU* 4.2 18.8 - - - +
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Residues in contact with VAL 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q TRP* 3.6 27.0 - - + -
33Q MET* 3.3 5.6 - - - -
34Q VAL* 3.0 41.5 + - + -
53Q PHE* 3.5 36.3 - - + -
55Q LEU* 4.4 12.1 - - + -
64Q ARG* 4.0 21.5 - - + +
66Q CYS* 5.1 0.4 - - - -
72Q LYS* 1.3 79.7 - - - +
74Q GLU* 1.3 62.8 + - - +
75Q GLU* 4.2 11.9 - - + -
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Residues in contact with GLU 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32Q TRP 3.7 4.9 - - - +
33Q MET* 3.5 32.1 - - + +
64Q ARG* 5.0 0.9 + - - -
72Q LYS* 4.2 18.8 - - - +
73Q VAL* 1.3 71.8 - - - +
75Q GLU* 1.3 75.6 + - - +
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Residues in contact with GLU 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Q ASP* 3.6 3.6 - - - +
32Q TRP* 2.7 76.2 + - + +
55Q LEU* 4.5 1.3 - - + -
59Q PHE* 3.9 20.0 - - + -
60Q PRO* 6.3 0.7 - - - -
64Q ARG* 3.1 38.5 + - - +
73Q VAL* 4.1 3.5 + - + -
74Q GLU* 1.3 82.7 - - - +
76Q SER* 1.3 66.1 + - - +
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Residues in contact with SER 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I KCR 4.1 3.1 - - - +
20Q ARG* 4.3 3.8 + - - -
24Q THR* 4.4 5.1 - - - +
28Q PHE* 3.9 32.7 - - - -
30Q HIS 3.2 7.9 - - - -
31Q ASP* 3.0 24.8 + - - +
32Q TRP* 4.2 3.6 - - - -
59Q PHE* 3.7 14.9 - - - -
75Q GLU* 1.3 83.3 + - - +
77Q GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I KCR 3.5 17.9 - - - -
28Q PHE* 4.0 6.7 - - - +
29Q THR 3.2 6.3 + - - -
30Q HIS* 2.9 36.4 + - - +
32Q TRP* 4.1 13.8 - - - +
76Q SER* 1.3 74.6 - - - +
78Q TYR* 1.3 61.3 + - - -
79Q ALA 3.7 1.1 - - - -
106Q LEU* 4.8 1.3 - - - -
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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