Contacts of the strand formed by residues 71 - 76 (chain B) in PDB entry 3SPD
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 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 3.9 1.7 - - - +
63B ASP* 3.0 47.4 + - + +
66B PRO* 3.6 24.3 - - + +
67B LYS* 3.0 29.6 + - + +
68B SER 4.2 2.4 + - - +
69B LYS 4.3 0.2 + - - -
70B MET* 1.3 76.5 - - - +
72B LEU* 1.3 77.7 + - - +
73B LEU* 4.2 0.2 - - + -
115B GLU* 5.5 0.6 + - - -
149B HIS* 2.9 26.3 + + + -
150B ILE 3.7 2.5 - - - -
151B MET* 3.8 21.2 - - + +
169B PHE* 3.6 25.4 - + - -
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Residues in contact with LEU 72 (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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52B ILE* 4.1 18.8 - - + -
60B LEU* 4.0 14.6 - - + -
61B VAL 3.5 5.4 - - - +
62B ARG* 3.9 18.4 - - + -
70B MET* 4.0 26.9 - - + -
71B HIS* 1.3 83.1 - - - +
73B LEU* 1.3 71.2 + - - +
112B ILE* 4.1 24.7 - - + -
115B GLU* 3.9 31.4 - - + +
149B HIS* 3.5 0.5 - - - -
150B ILE* 2.8 41.2 + - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 4.1 34.3 - - + -
41B TYR* 6.2 0.2 - - + -
59B VAL 3.4 2.3 - - - +
60B LEU* 3.3 6.8 - - - -
61B VAL* 2.8 54.1 + - + +
63B ASP* 3.7 33.2 - - + +
71B HIS* 3.9 1.8 - - - +
72B LEU* 1.3 86.8 - - - +
74B LEU* 1.3 59.4 + - - +
75B MET* 4.4 2.7 - - + -
147B HIS* 4.2 17.9 - - + -
148B LEU 3.4 2.9 - - - +
149B HIS* 3.5 32.5 - - + +
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Residues in contact with LEU 74 (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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58B VAL* 3.9 26.5 - - + -
59B VAL 3.4 16.2 - - - +
60B LEU* 4.0 4.5 - - + +
73B LEU* 1.3 70.8 - - - +
75B MET* 1.3 60.3 + - - +
76B THR 4.2 0.9 + - - -
100B LEU* 3.8 49.6 - - + +
103B TYR* 4.2 9.0 - - + -
104B VAL* 4.0 15.9 - - + -
108B LEU* 3.9 18.4 - - + -
137B PHE* 5.5 0.2 - - - -
146B LEU* 4.2 0.5 - - - +
147B HIS* 3.7 0.9 - - - -
148B LEU* 2.8 45.5 + - + +
150B ILE* 3.8 16.4 - - + +
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Residues in contact with MET 75 (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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38B LEU* 3.6 47.3 - - + +
41B TYR* 4.4 6.1 - - - -
42B ILE* 3.6 24.2 - - + +
58B VAL* 3.2 6.0 - - - -
59B VAL* 2.8 43.2 + - + +
61B VAL* 4.2 19.3 - - - -
73B LEU* 4.4 8.1 - - + +
74B LEU* 1.3 77.8 - - - +
76B THR* 1.3 64.5 + - - +
82B THR* 5.1 0.4 - - - +
145B ASN* 3.6 29.2 - - + +
146B LEU 3.7 12.8 - - - +
147B HIS* 3.9 10.1 - - + -
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Residues in contact with THR 76 (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 ILE* 3.4 17.7 - - - +
57B ASP 3.6 9.2 + - - -
58B VAL* 4.4 5.3 - - - +
74B LEU 4.2 1.2 + - - -
75B MET* 1.3 74.3 - - - +
77B ARG* 1.3 61.3 + - - +
78B ASP* 3.1 20.0 + - - +
81B LEU* 4.0 7.1 - - + +
82B THR* 3.8 34.0 + - - +
96B LEU* 4.3 22.4 - - - +
100B LEU* 5.0 5.4 - - - +
146B LEU* 3.9 27.4 + - + +
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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