Contacts of the strand formed by residues 30 - 37 (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 HIS 30 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16I PRO* 5.8 6.3 - - + -
17Q ALA 4.7 3.8 - - - -
18Q GLN 3.2 17.0 - - - +
19Q VAL* 3.3 24.0 - - + +
20Q ARG* 4.1 1.9 - - - -
28Q PHE* 4.5 0.5 - - - +
29Q THR* 1.3 99.8 + - + +
31Q ASP* 1.3 75.1 + - - +
32Q TRP* 4.2 1.3 - - + -
76Q SER* 3.2 3.5 - - - -
77Q GLY 2.9 32.9 + - - +
78Q TYR 4.3 7.0 + - - -
106Q LEU* 3.7 40.1 - - + +
107Q HIS 2.8 30.4 + - - -
108Q LEU* 5.4 2.2 - - - -
109Q GLU 6.0 0.2 - - - -
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Residues in contact with ASP 31 (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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16Q ARG 4.7 0.3 - - - -
17Q ALA* 3.6 0.3 - - - -
18Q GLN* 2.9 36.3 + - + +
19Q VAL 6.2 0.2 - - - -
20Q ARG* 2.9 44.5 + - + +
30Q HIS* 1.3 80.0 - - - +
32Q TRP* 1.3 60.8 + - - +
75Q GLU 3.6 5.2 - - - +
76Q SER* 3.0 18.4 + - - -
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Residues in contact with TRP 32 (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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16Q ARG 3.2 14.4 - - - +
17Q ALA* 4.2 11.7 - - + -
30Q HIS* 5.0 1.6 - - + -
31Q ASP* 1.3 76.2 - - - +
33Q MET* 1.3 70.6 + - - +
34Q VAL* 3.6 24.5 - - + -
55Q LEU* 3.6 24.5 - - + -
59Q PHE* 3.7 29.2 - + - -
73Q VAL* 3.6 13.9 - - + -
74Q GLU* 3.7 2.4 - - - +
75Q GLU* 2.7 65.8 + - + +
77Q GLY* 4.1 19.8 - - - +
79Q ALA 5.3 2.0 + - - -
81Q PHE* 4.0 11.8 - + - -
104Q LEU* 3.6 28.3 - - + +
106Q LEU* 4.3 20.2 - - + -
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Residues in contact with MET 33 (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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15Q HIS* 3.0 7.6 - - - +
16Q ARG* 3.0 62.4 + - + +
32Q TRP* 1.3 79.6 - - - +
34Q VAL* 1.3 71.0 + - - +
35Q PHE* 4.0 19.1 - - + -
72Q LYS* 3.5 40.8 - - + -
73Q VAL 3.3 7.9 - - - +
74Q GLU* 3.5 26.2 - - + +
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Residues in contact with VAL 34 (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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14Q GLY 3.4 13.0 - - - +
15Q HIS* 4.0 0.7 - - + -
32Q TRP* 3.6 19.7 - - + -
33Q MET* 1.3 76.9 - - - +
35Q PHE* 1.3 68.5 + - - +
53Q PHE* 3.9 24.1 - - + -
71Q TYR 4.0 0.2 - - - +
72Q LYS* 3.6 1.9 - - - -
73Q VAL* 3.0 46.5 + - + -
83Q LEU* 4.0 10.3 - - + -
85Q ILE* 4.6 2.9 - - + -
102Q TYR* 3.8 28.7 - - + -
104Q LEU* 3.9 12.6 - - + -
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Residues in contact with PHE 35 (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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12Q GLU 4.3 2.5 - - - -
13Q LEU* 3.6 2.8 - - - +
14Q GLY* 2.9 72.4 + - - +
15Q HIS* 3.7 7.6 - - - -
16Q ARG* 5.4 8.1 - - + -
33Q MET* 4.0 23.1 - - + -
34Q VAL* 1.3 78.5 - - - +
36Q VAL* 1.3 70.2 + - - +
37Q ARG* 3.5 57.7 - - + -
53Q PHE* 4.4 2.7 - - - -
70Q PRO* 6.5 0.2 - - + -
71Q TYR 3.3 10.1 - - - +
72Q LYS* 4.8 7.6 - - + +
85Q ILE* 5.2 0.5 - - - +
115Q ASN* 5.5 4.0 - - - -
116Q HIS 4.7 2.0 - - - -
117Q LEU* 4.0 11.9 - - + -
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Residues in contact with VAL 36 (chain Q).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11Q LEU* 4.9 9.2 - - + -
12Q GLU 3.5 7.6 - - - +
13Q LEU* 3.7 23.1 - - + -
35Q PHE* 1.3 81.6 - - - +
37Q ARG* 1.3 65.5 + - - +
44Q ILE* 4.6 10.3 - - + -
51Q VAL* 3.9 10.8 - - + -
53Q PHE* 3.9 11.4 - - + -
71Q TYR* 3.1 40.4 + - + +
85Q ILE* 3.9 22.7 - - + -
87Q VAL* 4.4 19.3 - - + -
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Residues in contact with ARG 37 (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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116N HIS* 4.3 11.8 + - - -
117N LEU* 3.1 31.7 + - - +
201N SO4 4.0 26.7 + - - -
11Q LEU* 3.5 2.4 - - - +
12Q GLU* 2.6 65.2 + - + +
35Q PHE* 3.5 40.0 - - + -
36Q VAL* 1.3 77.7 - - - +
38Q GLY* 1.3 65.7 + - - +
40Q GLU* 5.7 1.3 - - - +
44Q ILE* 3.8 11.4 - - - -
71Q TYR* 5.4 0.2 - - - -
117Q LEU* 3.6 15.6 - - - +
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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