Contacts of the strand formed by residues 49 - 55 (chain A) in PDB entry 2DLH
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 ILE 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A PRO* 4.8 1.3 - - + -
41A GLU* 5.0 5.4 - - + -
42A PRO* 4.3 23.6 - - + -
45A PRO* 4.4 13.7 - - + -
47A GLY 3.2 7.1 + - - +
48A GLN* 1.3 73.9 - - - +
50A GLN* 1.3 66.1 + - - +
51A GLY 3.4 25.4 - - - +
52A TYR* 3.6 29.4 - - + +
74A ASP* 4.4 15.7 - - - +
95A ALA* 4.6 8.1 - - + -
96A PHE 4.0 3.6 - - - +
97A THR* 3.2 26.5 - - + -
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Residues in contact with GLN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLN* 3.6 27.4 + - - +
49A ILE* 1.3 76.0 + - - +
51A GLY* 1.3 57.9 + - - +
72A VAL 5.0 0.2 - - - +
73A ALA* 4.3 5.9 - - - +
74A ASP* 4.0 13.4 + - - +
96A PHE* 3.7 21.4 + - + +
97A THR 4.4 1.1 - - - -
98A SER* 3.9 30.5 - - - +
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ILE* 3.4 10.8 - - - +
50A GLN* 1.3 81.6 - - - +
52A TYR* 1.3 79.8 + - - -
72A VAL 4.2 4.9 - - - -
74A ASP* 3.6 18.2 - - - -
96A PHE* 3.2 25.8 + - - +
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PRO* 5.8 1.3 - - + -
39A TRP* 3.8 42.2 - + + +
41A GLU* 2.9 33.5 + - + +
42A PRO* 4.4 8.5 - - + -
49A ILE* 3.6 16.0 - - + +
51A GLY* 1.3 82.4 - - - -
53A ARG* 1.3 61.9 + - - +
71A ASN* 5.1 0.7 + - - -
72A VAL* 3.3 43.6 + - + +
74A ASP* 3.7 25.5 + - - -
75A SER 4.7 0.2 - - - -
76A GLN* 4.3 9.9 + - + -
93A VAL* 4.7 1.1 - - + -
94A LEU 3.2 22.0 - - - +
95A ALA* 3.7 20.4 - - + -
96A PHE* 3.1 15.8 - - - -
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Residues in contact with ARG 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 1.3 79.0 + - - +
54A VAL* 1.3 68.3 + - - +
55A TYR* 2.9 43.4 + - + +
69A LYS* 4.5 19.5 - - + +
70A HIS 4.4 12.4 + - - +
72A VAL* 4.9 0.2 - - - -
93A VAL* 3.5 5.9 - - - +
94A LEU* 3.3 37.1 + - + -
96A PHE* 4.3 11.3 - - + -
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Residues in contact with VAL 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 5.2 1.6 - - + -
39A TRP* 3.7 32.1 - - + -
53A ARG* 1.3 79.9 - - - +
55A TYR* 1.3 72.7 + - - +
56A TYR* 4.5 7.0 - - + -
69A LYS* 3.2 5.5 - - - +
70A HIS* 2.8 48.8 + - + +
72A VAL* 3.7 14.3 - - + +
78A THR* 4.3 9.9 - - + -
80A ILE* 4.8 6.3 - - + -
91A VAL* 4.3 17.7 - - + -
92A LYS 3.2 13.9 - - - +
93A VAL* 4.4 2.7 - - + -
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ARG* 2.9 45.7 + - + -
54A VAL* 1.3 79.2 - - - +
56A TYR* 1.3 60.2 + - - +
64A VAL* 3.7 30.5 - - + -
67A TRP* 3.5 24.7 - - + -
69A LYS* 3.8 29.8 - - + +
91A VAL* 3.3 6.2 - - - -
92A LYS* 2.9 40.2 + - + -
94A LEU* 3.1 22.0 - - + +
104A LEU* 3.3 32.5 - - + -
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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