Contacts of the strand formed by residues 5 - 14 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1F MET* 3.1 27.2 - - + -
3F LYS* 3.5 29.2 + - - -
4K PRO* 1.3 71.8 - - - +
6K VAL* 1.3 55.0 + - - +
37K HIS* 3.0 28.6 + + - +
77K THR* 3.1 34.1 - - + +
78K PRO* 2.9 16.3 + - + +
79K PHE* 3.2 22.4 - + + -
80K LEU* 2.7 32.7 + - - +
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Residues in contact with VAL 6 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F PHE 5.7 1.9 + - - +
3F LYS* 5.4 1.8 - - - +
4F PRO* 3.8 24.7 - - + +
6F VAL* 4.5 2.9 - - + -
80F LEU* 3.9 16.2 - - + -
4K PRO 3.4 5.2 + - - +
5K HIS* 1.3 75.9 - - - +
7K THR* 1.3 65.4 + - - +
37K HIS* 3.8 4.5 - - - -
38K LEU* 3.0 39.0 + - + +
44K LEU* 3.9 15.3 - - + -
80K LEU* 3.3 20.9 - - + +
82K PHE* 3.5 30.1 - - + -
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Residues in contact with THR 7 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K HIS 4.1 0.2 + - - -
6K VAL* 1.3 78.6 - - - +
8K VAL* 1.3 68.9 + - - +
36K GLY 3.0 22.2 - - - +
37K HIS* 3.9 11.2 - - + +
38K LEU* 4.5 0.9 - - - +
79K PHE* 3.6 31.1 - - + -
80K LEU 2.7 12.0 + - - +
81K ARG* 3.1 17.5 - - - +
82K PHE* 2.9 27.8 + - - -
158K SO4 2.8 28.1 + - - +
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Residues in contact with VAL 8 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7K THR* 1.3 82.5 - - - +
9K ALA* 1.3 62.6 + - - +
34K PRO 4.8 0.2 - - - -
35K ALA* 3.1 5.2 - - - +
36K GLY 2.9 38.2 + - - +
37K HIS 5.0 2.9 - - - +
38K LEU* 5.6 2.0 - - + -
44K LEU* 3.6 42.0 - - + +
47K ALA* 4.1 15.0 - - + +
48K ALA* 3.9 24.5 - - + +
51K GLU* 4.4 7.9 - - + -
81K ARG* 5.1 1.1 - - - -
82K PHE* 3.2 7.4 - - + +
84K PHE* 4.2 11.4 - - + -
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Residues in contact with ALA 9 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K VAL* 1.3 78.1 - - - +
10K CYS* 1.3 69.6 + - - +
33K GLN* 4.2 3.8 - - + -
34K PRO 3.6 7.9 - - - -
35K ALA* 4.0 5.8 - - + -
81K ARG* 3.4 36.6 - - - +
82K PHE 2.9 7.6 + - - +
83K LEU* 4.0 11.9 - - + -
84K PHE* 2.7 28.8 + - - +
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Residues in contact with CYS 10 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ALA* 1.3 84.4 - - - +
11K VAL* 1.3 64.1 + - - +
12K VAL* 3.6 22.1 + - + -
19K LEU 4.8 0.7 - - - +
33K GLN* 3.4 18.4 - - - +
34K PRO* 3.5 24.2 + - + +
48K ALA* 4.2 32.1 - - - -
52K LEU* 4.4 10.5 - - + -
62K PRO* 4.9 1.1 - - - -
84K PHE* 3.3 8.7 - - - +
86K ILE* 3.8 22.4 - - + -
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Residues in contact with VAL 11 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K CYS* 1.3 74.1 - - - +
12K VAL* 1.3 53.8 + - - +
13K HIS* 4.7 1.0 - - + +
18K PHE* 3.5 28.3 - - + -
19K LEU 5.9 0.4 - - - -
33K GLN* 4.6 6.5 - - + +
66K ILE* 4.5 3.4 - - + -
83K LEU* 3.9 19.5 - - + -
84K PHE 2.7 13.3 + - - +
85K ALA 3.4 1.0 - - - -
86K ILE 2.6 34.5 + - - +
126K SER* 3.9 29.4 - - - +
127K ILE* 4.8 4.3 - - + -
130K TYR* 3.4 35.1 - - + -
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Residues in contact with VAL 12 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K CYS* 3.6 25.2 + - + +
11K VAL* 1.3 76.0 - - - +
13K HIS* 1.3 61.3 + - - +
18K PHE* 3.4 6.2 - - - +
19K LEU* 3.1 50.4 + - + +
34K PRO* 4.9 3.8 - - + -
52K LEU* 4.5 11.7 - - + -
58K ILE* 5.5 2.0 - - + -
86K ILE* 3.2 21.3 - - + +
88K LEU* 3.7 31.4 - - + -
106K TRP* 3.7 13.1 - - + -
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Residues in contact with HIS 13 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 4.6 9.5 + - - -
11K VAL* 4.7 1.1 - - + -
12K VAL* 1.3 76.7 - - - +
14K ALA* 1.3 62.7 + - - +
15K GLU 5.4 0.4 - - - -
16K GLY* 3.7 30.5 + - - -
17K LYS 3.4 9.3 + - - -
18K PHE* 3.2 37.6 - + + -
86K ILE 2.7 10.9 + - - +
87K GLU* 2.8 31.5 - - - +
88K LEU 3.1 24.4 + - - +
130K TYR* 3.0 24.0 + + + +
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Residues in contact with ALA 14 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K HIS* 1.3 79.5 - - - +
15K GLU* 1.3 71.5 + - - +
16K GLY 3.1 2.5 - - - -
17K LYS* 2.8 24.9 + - - +
88K LEU* 3.7 19.5 - - + +
90K GLN* 3.7 4.7 - - - +
91K ILE* 3.6 29.1 - - + +
106K TRP* 4.0 16.9 - - + -
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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