Contacts of the strand formed by residues 5 - 14 (chain G) in PDB entry 3SHD
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 5 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 3.1 24.8 - - - -
3C LYS* 3.4 32.5 + - + -
3G LYS 5.4 0.2 - - - -
4G PRO* 1.3 74.1 - - - +
6G VAL* 1.3 62.4 + - - +
7G THR 4.1 0.2 - - - -
37G HIS* 2.5 32.3 + + + +
77G THR* 3.6 29.2 - - + +
78G PRO* 2.8 21.7 + - + +
79G PHE* 3.4 14.8 - + + +
80G LEU 2.8 26.0 + - - +
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Residues in contact with VAL 6 (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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2C PHE 5.3 3.4 + - - +
3C LYS* 5.3 1.6 - - - +
4C PRO* 3.3 37.5 - - + +
6C VAL* 4.7 0.2 - - + -
80C LEU* 4.0 9.4 - - + -
4G PRO* 3.9 15.7 + - + +
5G HIS* 1.3 77.2 - - - +
7G THR* 1.3 69.2 + - - +
37G HIS* 3.4 5.9 - - - +
38G LEU* 3.0 41.4 + - + +
44G LEU* 4.0 8.3 - - + -
80G LEU* 3.4 7.9 - - + +
82G PHE* 3.9 27.6 - - + -
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Residues in contact with THR 7 (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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6G VAL* 1.3 79.1 - - - +
8G VAL* 1.3 68.8 + - - +
36G GLY 3.3 11.0 - - - +
37G HIS* 3.3 35.2 - - + +
38G LEU 4.4 0.2 - - - +
79G PHE* 3.4 25.3 - - + -
80G LEU 2.9 9.9 + - - +
81G ARG* 3.2 17.9 - - - +
82G PHE* 3.0 24.3 + - - -
157G SO4 3.0 23.0 + - - +
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Residues in contact with VAL 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G THR* 1.3 81.5 - - - +
9G ALA* 1.3 64.7 + - - +
35G ALA* 3.2 1.5 - - - +
36G GLY 2.8 41.3 + - - +
37G HIS 4.7 0.7 - - - +
38G LEU* 5.2 3.8 - - + -
44G LEU* 3.9 37.7 - - + +
47G ALA* 3.6 16.4 - - + +
48G ALA* 3.5 36.8 - - + +
51G GLU* 4.9 1.8 - - + -
81G ARG* 4.9 0.4 - - - -
82G PHE* 3.3 16.6 - - + +
84G PHE* 4.3 3.8 - - + -
157G SO4 4.1 1.4 + - - -
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Residues in contact with ALA 9 (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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8G VAL* 1.3 79.7 - - - +
10G CYS* 1.3 65.0 + - - +
33G GLN* 4.5 2.0 - - + -
34G PRO 3.6 1.6 - - - -
35G ALA* 3.4 20.6 - - + +
48G ALA* 6.1 0.2 - - - +
81G ARG* 3.5 34.1 - - + +
82G PHE 2.8 11.1 + - - +
83G LEU* 3.4 8.2 - - + +
84G PHE* 3.0 27.6 + - - -
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Residues in contact with CYS 10 (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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9G ALA* 1.3 81.4 - - - +
11G VAL* 1.3 61.8 + - - +
12G VAL* 3.5 17.9 + - + -
19G LEU 4.8 0.2 - - - +
33G GLN* 3.4 7.7 - - - +
34G PRO* 3.0 37.1 + - + +
48G ALA* 4.1 33.4 - - - -
52G LEU* 4.9 7.2 - - + -
62G PRO* 4.4 2.5 - - - -
84G PHE* 3.5 13.5 - - - +
86G ILE* 3.8 23.1 - - + -
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Residues in contact with VAL 11 (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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10G CYS* 1.3 69.6 - - - +
12G VAL* 1.3 63.2 + - - +
13G HIS* 3.4 3.1 + - - +
18G PHE* 3.9 21.8 - - + -
19G LEU 5.8 0.2 - - - -
33G GLN* 4.3 17.0 - - - +
66G ILE* 4.1 7.9 - - + -
83G LEU* 3.8 30.3 - - + -
84G PHE 2.9 14.1 + - - +
85G ALA* 3.9 1.3 - - - +
86G ILE 3.1 19.2 + - - +
126G SER 4.2 13.5 - - - +
127G ILE* 5.2 3.1 - - + -
130G TYR* 3.6 33.9 - - + -
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Residues in contact with VAL 12 (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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10G CYS* 3.5 18.9 + - + +
11G VAL* 1.3 73.9 - - - +
13G HIS* 1.3 60.0 + - - +
14G ALA 4.4 0.4 - - - -
18G PHE* 3.6 6.4 - - - +
19G LEU* 3.2 41.6 + - + +
34G PRO* 4.6 1.6 - - + -
52G LEU* 3.9 29.4 - - + -
58G ILE* 6.0 5.4 - - + -
86G ILE* 3.5 25.8 - - + +
88G LEU* 3.9 26.9 - - + -
106G TRP* 4.0 12.8 - - + -
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Residues in contact with HIS 13 (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 VAL 4.2 4.5 - - - +
12G VAL* 1.3 76.8 - - - +
14G ALA* 1.3 61.6 + - - +
15G GLU 5.1 0.8 + - - -
16G GLY* 4.2 23.2 + - - -
17G LYS 3.6 9.0 + - - -
18G PHE* 3.4 34.5 - + + -
86G ILE 2.9 12.2 + - - +
87G GLU* 2.6 33.7 - - - +
88G LEU* 3.0 29.4 + - - +
106G TRP* 4.2 1.1 - - - -
130G TYR* 3.3 18.4 - + + +
113L LEU* 5.1 7.1 + - + +
114L GLN* 4.2 16.5 + - - -
128L ARG* 3.5 15.2 + - - -
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Residues in contact with ALA 14 (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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13G HIS* 1.3 78.4 - - - +
15G GLU* 1.3 63.5 + - - +
16G GLY 3.1 3.4 - - - -
17G LYS* 2.7 38.8 + - - +
88G LEU* 3.7 23.3 - - + -
90G GLN* 3.9 20.9 - - - +
91G ILE* 3.7 4.8 - - + +
106G TRP* 3.5 21.2 - - + -
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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