Contacts of the strand formed by residues 5 - 14 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.2 35.1 - - + +
2A PHE 5.7 0.7 - - - -
3A LYS* 3.2 38.1 + - - +
4I PRO* 1.3 73.0 - - - +
6I VAL* 1.3 62.0 + - - +
7I THR 4.0 0.4 + - - -
37I HIS* 3.2 26.7 + + + +
77I THR* 3.7 24.7 - - + +
78I PRO* 3.1 23.3 + - + +
79I PHE* 3.6 19.7 - + + -
80I LEU* 3.1 25.3 + - - +
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Residues in contact with VAL 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A PHE 5.3 4.6 + - - +
4A PRO* 3.9 20.0 - - + +
6A VAL* 5.0 0.9 - - + -
80A LEU* 3.7 19.7 - - + -
4I PRO* 3.8 4.4 + - + +
5I HIS* 1.3 78.3 - - - +
7I THR* 1.3 58.2 + - - +
37I HIS* 3.5 5.9 - - - +
38I LEU* 2.6 62.5 + - + +
44I LEU* 3.8 17.3 - - + -
80I LEU* 3.5 21.5 - - + -
82I PHE* 3.9 11.9 - - + -
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Residues in contact with THR 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I VAL* 1.3 77.8 - - - +
8I VAL* 1.3 59.9 + - - +
36I GLY 2.9 17.3 - - - +
37I HIS* 4.0 12.8 - - + +
79I PHE* 3.4 36.8 - - + -
80I LEU 2.9 6.9 + - - +
81I ARG* 3.1 27.9 - - - +
82I PHE* 2.9 29.1 + - - -
158I SO4 3.4 22.0 + - - +
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Residues in contact with VAL 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I THR* 1.3 76.6 - - - +
9I ALA* 1.3 60.8 + - - +
35I ALA* 3.0 5.9 - - - +
36I GLY 2.8 43.7 + - - -
37I HIS 4.5 3.4 - - - +
38I LEU* 5.4 2.0 - - + -
44I LEU* 3.6 44.6 - - + +
47I ALA* 3.8 15.7 - - + +
48I ALA* 3.6 31.2 - - + +
51I GLU* 4.2 7.6 - - + -
82I PHE* 3.5 4.0 - - + -
84I PHE* 4.2 8.1 - - + -
158I SO4 5.0 0.2 - - - -
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Residues in contact with ALA 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I VAL* 1.3 75.3 - - - +
10I CYS* 1.3 73.8 + - - +
33I GLN* 4.6 0.4 - - + -
34I PRO 4.5 0.9 - - - -
35I ALA* 3.9 7.6 - - + +
48I ALA* 5.1 0.7 - - - -
81I ARG* 3.1 42.4 - - - +
82I PHE 2.9 14.8 + - - +
83I LEU* 3.9 13.2 - - + -
84I PHE* 3.2 23.8 + - - -
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Residues in contact with CYS 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I ALA* 1.3 85.2 - - - +
11I VAL* 1.3 62.3 + - - +
12I VAL* 3.4 19.8 + - + -
19I LEU 4.7 0.7 - - - +
33I GLN* 3.5 12.1 - - - +
34I PRO* 3.3 40.7 + - + +
48I ALA* 4.0 25.4 - - - +
52I LEU* 4.9 4.0 - - + -
62I PRO* 4.6 2.0 - - - -
84I PHE* 4.0 13.0 - - - -
86I ILE* 3.3 25.8 - - + -
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Residues in contact with VAL 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I CYS* 1.3 70.2 - - - +
12I VAL* 1.3 58.2 + - - +
13I HIS 3.8 0.3 + - - -
18I PHE* 3.9 18.4 - - + -
19I LEU 5.8 0.7 - - - -
33I GLN* 4.2 12.8 - - + -
66I ILE* 4.3 4.7 - - + -
83I LEU* 3.6 27.1 - - + -
84I PHE 3.1 14.5 + - - +
85I ALA* 3.6 2.1 - - - +
86I ILE 3.2 21.8 + - - +
126I SER* 4.0 18.4 - - - +
127I ILE* 4.4 7.4 - - + -
130I TYR* 3.3 37.5 - - + -
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Residues in contact with VAL 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I CYS* 3.4 29.7 + - + +
11I VAL* 1.3 73.0 - - - +
13I HIS* 1.3 61.1 + - - +
18I PHE* 3.5 5.1 - - - +
19I LEU* 3.0 40.4 + - + +
34I PRO* 4.2 6.3 - - + -
52I LEU* 4.1 17.5 - - + -
58I ILE* 5.1 4.7 - - + -
86I ILE* 3.2 34.5 - - + +
88I LEU* 4.1 21.3 - - + -
106I TRP* 4.1 8.1 - - + -
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Residues in contact with HIS 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F ARG* 5.0 5.0 + - - -
11I VAL 4.5 0.2 - - - +
12I VAL* 1.3 75.9 - - - +
14I ALA* 1.3 62.9 + - - +
15I GLU 4.5 0.6 + - - -
16I GLY* 3.9 27.3 + - - -
17I LYS 3.2 19.3 + - - +
18I PHE* 3.3 29.6 - + + -
86I ILE 2.7 14.4 + - - +
87I GLU* 2.9 29.4 + - - +
88I LEU* 2.7 34.0 + - - +
106I TRP* 4.8 2.2 - - - -
130I TYR* 3.4 27.7 + + + +
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Residues in contact with ALA 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I HIS* 1.3 81.8 - - - +
15I GLU* 1.3 73.3 + - - +
16I GLY 3.3 2.0 - - - -
17I LYS* 2.8 28.2 + - - +
88I LEU* 3.8 28.0 - - + +
90I GLN* 4.4 2.5 - - - -
91I ILE* 3.6 31.8 - - + +
106I TRP* 4.5 4.3 - - + -
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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
------------------------------------------------------------
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