Contacts of the strand formed by residues 19 - 25 (chain I) in PDB entry 6D6U
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 VAL 19 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11I MET* 3.5 31.4 - - + -
13I MET* 3.7 28.5 - - + -
17I GLU 3.6 11.6 + - - +
18I ARG* 1.3 81.9 - - - +
20I THR* 1.3 66.8 + - - +
21I LEU* 3.7 14.6 - - + -
73I LEU 3.9 0.5 - - - +
74I THR* 3.3 7.2 - - - +
75I ILE* 3.0 47.4 + - + -
78I VAL* 4.9 11.9 - - + -
103I LEU* 4.6 3.1 - - + -
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Residues in contact with THR 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I PRO* 4.4 11.1 - - - +
11I MET* 5.5 2.4 - - - +
18I ARG* 4.5 9.7 + - - +
19I VAL* 1.3 78.9 + - - +
21I LEU* 1.3 71.0 + - - +
22I SER* 5.8 2.0 - - - -
72I THR* 3.7 24.5 - - + -
73I LEU 3.9 2.0 - - - -
74I THR* 3.9 12.2 + - - +
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Residues in contact with LEU 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 4.5 5.2 - - - +
7I SER 4.5 4.0 - - - +
8I PRO* 4.7 4.0 - - + -
11I MET* 4.5 7.2 - - + -
19I VAL* 3.7 22.9 - - + -
20I THR* 1.3 83.9 - - - +
22I SER* 1.3 62.7 + - - +
35I TRP* 4.7 8.7 - - + -
72I THR* 3.3 13.5 - - - +
73I LEU* 2.9 48.0 + - + +
75I ILE* 4.6 12.8 - - + -
86I TYR* 4.1 26.5 - - + -
101I THR* 4.0 36.8 - - + +
103I LEU* 5.1 1.6 - - + -
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Residues in contact with SER 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I GLN* 3.5 8.3 + - - +
7I SER* 2.6 55.4 + - - +
20I THR* 5.8 2.0 - - - -
21I LEU* 1.3 76.9 - - - +
23I CYS* 1.3 62.3 + - - +
24I LYS 4.2 0.4 + - - -
35I TRP* 4.3 2.7 - - - -
71I PHE 3.5 12.3 - - - -
72I THR* 4.6 3.4 - - - +
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Residues in contact with CYS 23 (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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4I MET* 3.5 27.1 - - - -
5I THR 3.4 11.2 - - - -
6I GLN* 4.3 0.4 - - - +
22I SER* 1.3 76.2 - - - +
24I LYS* 1.3 60.7 + - - +
33I VAL* 5.5 0.9 - - + -
35I TRP* 3.6 13.9 - - + -
69I THR 3.8 0.2 - - - +
71I PHE* 3.5 37.6 + - + +
88I CYS* 2.0 55.2 - - + -
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Residues in contact with LYS 24 (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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4I MET* 3.6 3.4 - - - +
5I THR* 2.4 62.4 + - + +
22I SER* 4.2 1.0 - - - -
23I CYS* 1.3 72.3 - - - +
25I ALA* 1.3 75.0 + - - +
26I SER* 4.3 1.7 + - - +
69I THR* 4.3 9.9 - - - +
70I ASP* 3.2 27.3 + - - +
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Residues in contact with ALA 25 (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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2I ILE* 5.4 1.1 - - + -
3I VAL 4.0 0.2 - - - -
4I MET* 3.5 29.4 - - + -
24I LYS* 1.3 82.7 - - - +
26I SER* 1.3 66.6 + - - +
27I GLU 3.4 8.8 - - - +
29I VAL* 3.6 28.0 - - + -
69I THR* 3.6 27.9 + - - +
71I PHE* 4.5 0.9 - - + -
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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
------------------------------------------------------------
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