Contacts of the strand formed by residues 30 - 37 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17G ALA 5.1 2.2 - - - -
18G GLN 3.4 13.2 - - - +
19G VAL* 3.5 25.7 - - + +
20G ARG* 4.0 2.1 - - - -
29G THR* 1.3 105.6 + - - +
31G ASP* 1.3 74.3 + - - +
32G TRP* 4.2 2.2 - - + -
76G SER* 3.3 2.4 - - - -
77G GLY 2.8 36.3 + - - +
78G TYR 4.5 4.4 + - - -
106G LEU* 3.7 43.3 - - + +
107G HIS 2.9 28.0 + - - -
108G LEU* 5.6 2.5 - - - -
109G GLU 5.8 0.7 - - - -
16L PRO* 5.2 8.7 - - + -
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Residues in contact with ASP 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G ARG 4.2 0.3 - - - +
18G GLN* 2.7 45.7 + - + +
20G ARG* 2.8 40.2 + - + +
30G HIS* 1.3 78.2 - - - +
32G TRP* 1.3 60.6 + - - +
75G GLU 3.9 7.2 - - - +
76G SER* 2.7 26.7 + - - -
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Residues in contact with TRP 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G HIS* 5.0 0.9 - - + -
16G ARG 3.0 14.8 - - - +
17G ALA* 3.9 11.7 - - + -
30G HIS* 4.8 2.5 - - + -
31G ASP* 1.3 76.1 - - - +
33G MET* 1.3 68.7 + - - +
34G VAL* 3.9 15.9 - - + -
55G LEU* 3.9 23.3 - - + -
59G PHE* 3.7 25.4 - + - -
73G VAL* 4.0 13.0 - - + -
74G GLU* 3.8 1.2 - - - +
75G GLU* 3.2 48.7 + - + +
77G GLY* 4.4 22.8 - - - +
79G ALA 4.8 3.8 + - - -
81G PHE* 4.0 14.0 - + - -
104G LEU* 3.6 44.6 - - + +
106G LEU* 3.9 18.8 - - + -
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Residues in contact with MET 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G HIS* 3.1 5.1 - - - -
16G ARG* 2.9 76.0 + - + +
32G TRP* 1.3 77.6 - - - +
34G VAL* 1.3 61.9 + - - +
35G PHE* 3.5 23.1 - - + -
72G LYS* 4.0 13.7 - - + +
73G VAL 3.2 13.5 - - - +
74G GLU* 3.6 24.7 - - + +
201G SO4 3.8 15.7 - - - +
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Residues in contact with VAL 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G GLY 3.5 11.7 - - - +
15G HIS* 3.8 7.6 - - + -
32G TRP* 3.9 19.5 - - + -
33G MET* 1.3 73.7 - - - +
35G PHE* 1.3 65.7 + - - +
53G PHE* 3.9 28.0 - - + -
72G LYS* 3.1 4.5 - - - +
73G VAL* 2.8 38.4 + - + -
83G LEU* 4.1 11.2 - - + -
85G ILE* 4.4 8.5 - - + -
102G TYR* 4.0 21.3 - - + -
104G LEU* 3.8 13.5 - - + -
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Residues in contact with PHE 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G GLU* 4.4 3.1 - - - -
13G LEU* 3.7 1.6 - - - +
14G GLY* 2.9 63.0 + - - +
15G HIS* 3.7 5.6 - - - -
16G ARG* 4.2 16.4 - - - -
33G MET* 3.5 20.6 - - + -
34G VAL* 1.3 79.4 - - - +
36G VAL* 1.3 72.7 + - - +
37G ARG* 3.7 46.2 - - + -
53G PHE* 4.2 2.9 - - - -
71G TYR 3.3 12.1 - - - +
72G LYS* 3.8 2.7 - - + -
85G ILE* 5.1 0.5 - - - +
115G ASN* 5.6 0.7 - - - -
116G HIS 5.0 0.2 - - - -
117G LEU* 3.6 26.9 - - + -
201G SO4 3.7 31.0 - - - +
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Residues in contact with VAL 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G LEU* 4.5 9.4 - - + -
12G GLU 3.3 6.7 - - - +
13G LEU* 3.8 27.8 - - + -
35G PHE* 1.3 81.3 - - - +
37G ARG* 1.3 67.6 + - - +
44G ILE* 4.4 12.6 - - + -
51G VAL* 4.3 15.7 - - + -
53G PHE* 4.2 4.2 - - + -
71G TYR* 2.9 33.5 + - - +
85G ILE* 4.0 29.2 - - + -
87G VAL* 4.4 17.7 - - + -
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Residues in contact with ARG 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A ASN* 4.6 5.7 + - - +
11G LEU* 3.5 3.2 - - - +
12G GLU* 2.6 70.2 + - + +
16G ARG* 4.6 7.1 - - - +
35G PHE* 3.7 27.8 - - + -
36G VAL* 1.3 77.3 - - - +
38G GLY* 1.3 65.2 + - - +
44G ILE* 3.8 13.7 - - - -
71G TYR* 5.4 0.4 - - + -
117G LEU* 4.2 15.4 - - - +
201G SO4 3.2 39.9 + - - +
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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