Contacts of the strand formed by residues 61 - 69 (chain B) in PDB entry 2HHL
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 THR 61 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B GLU* 4.0 1.3 - - - +
58B ILE 2.7 56.2 + - - +
59B ASP* 3.1 8.0 - - + +
60B GLY* 1.3 79.4 - - - +
62B ILE* 1.3 63.8 + - - +
63B HIS* 3.3 24.6 + - + +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PRO* 3.7 34.3 - - + +
56B VAL 3.5 4.3 - - - +
57B GLU* 4.3 26.7 - - + +
60B GLY 5.4 1.6 - - - +
61B THR* 1.3 78.1 + - - +
63B HIS* 1.3 64.7 + - - +
64B GLN* 3.9 15.5 + - - +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 3.7 31.4 - + + -
54B VAL 3.6 0.3 - - - +
55B PRO* 3.4 0.3 - - - +
56B VAL* 2.7 41.6 + - - +
58B ILE* 3.7 27.8 - - + +
61B THR* 3.3 41.4 + - + +
62B ILE* 1.3 76.6 - - - +
64B GLN* 1.3 63.2 + - - +
65B VAL* 3.7 0.5 + - - +
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PHE* 3.9 15.4 - - - +
53B ILE* 3.2 24.0 - - + +
54B VAL 3.7 1.3 - - - -
55B PRO* 4.0 14.0 - - - +
62B ILE* 3.9 22.6 + - - +
63B HIS* 1.3 74.1 - - - +
65B VAL* 1.3 62.0 + - - +
66B TYR* 3.8 37.2 - - + +
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Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B SER* 3.6 31.6 - - - +
43B SER 3.7 7.9 - - - +
44B PHE* 3.9 23.1 - - + -
52B PHE 3.8 0.5 - - - +
53B ILE* 3.3 6.0 - - - -
54B VAL* 2.6 48.0 + - + +
56B VAL* 3.9 20.6 - - + -
58B ILE* 6.0 0.2 - - + -
63B HIS 4.1 2.9 - - - +
64B GLN* 1.3 78.0 - - - +
66B TYR* 1.3 64.2 + - - +
67B VAL* 3.9 5.3 - - + +
96B TYR* 3.9 16.8 - - + -
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B HIS 3.9 1.6 - - - +
42B SER* 3.2 3.5 - - - -
43B SER* 2.8 43.7 + - - +
44B PHE 3.8 9.6 - - - -
45B LYS 3.9 9.0 - - - +
46B PRO* 3.6 39.4 - - + +
47B ILE* 3.8 35.7 - - + +
50B ALA* 4.0 9.6 - - + -
52B PHE 3.7 3.1 - - - -
53B ILE* 3.7 31.1 - - + +
64B GLN* 3.8 36.5 - - + +
65B VAL* 1.3 72.3 - - - +
67B VAL* 1.3 61.5 + - - +
68B LEU* 4.1 0.5 + - - +
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Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.7 28.3 - - + -
41B HIS 3.8 2.5 - - - +
42B SER* 3.3 24.2 - - - +
50B ALA* 4.0 1.9 - - - +
51B ASP* 2.7 34.0 + - - +
52B PHE* 2.8 48.5 + - + +
54B VAL* 4.6 3.4 - - + -
65B VAL* 3.9 14.4 - - + +
66B TYR* 1.3 75.5 - - - +
68B LEU* 1.3 59.9 + - - +
100B VAL* 4.1 21.3 - - + -
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Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 3.2 7.3 - - - +
41B HIS* 2.9 39.9 + - + +
47B ILE* 3.9 18.2 - - + -
49B ASN* 3.5 43.3 - - - +
50B ALA* 4.0 7.4 - - - -
51B ASP* 3.3 9.2 - - - +
66B TYR 4.1 0.4 + - - -
67B VAL* 1.3 74.2 - - - +
69B LYS* 1.3 61.2 + - - +
163B TRP* 3.6 15.1 - - + -
164B PHE 4.1 5.6 - - - +
165B ASP* 3.9 31.0 - - + +
167B MET* 5.5 8.1 - - - -
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B LEU 4.1 4.5 - - - -
40B VAL* 4.5 1.3 - - - -
51B ASP* 2.8 38.5 + - + +
52B PHE* 3.6 33.6 - - + -
68B LEU* 1.3 73.0 - - - +
70B ARG* 1.3 65.3 + - - +
71B PRO* 3.6 1.2 - - - +
73B VAL* 3.5 17.3 - - + -
74B ASP* 2.7 41.6 + - - -
104B LEU* 4.3 9.4 - - + +
106B ARG* 4.2 9.1 - - - +
163B TRP* 3.2 12.6 - - - -
167B MET* 4.3 9.9 - - - +
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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