Contacts of the strand formed by residues 71 - 76 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ARG* 3.9 1.9 - - - +
63A ASP* 3.0 48.8 + - + +
66A PRO* 3.6 24.8 - - + +
67A LYS* 3.0 29.4 + - + +
68A SER 4.2 1.8 + - - +
69A LYS 4.2 0.4 - - - -
70A MET* 1.3 77.8 - - - +
72A LEU* 1.3 77.1 + - - +
73A LEU* 3.9 0.6 - - + +
115A GLU* 5.5 0.6 + - - -
149A HIS* 2.9 25.9 + + + -
150A ILE 3.7 2.9 - - - -
151A MET* 3.9 18.6 - - + +
169A PHE* 3.7 25.1 - + - -
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Residues in contact with LEU 72 (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 ILE* 4.0 18.8 - - + -
60A LEU* 4.0 15.0 - - + -
61A VAL 3.4 5.2 - - - +
62A ARG* 4.0 16.8 - - + -
70A MET* 4.0 26.5 - - + -
71A HIS* 1.3 82.5 - - - +
73A LEU* 1.3 71.0 + - - +
112A ILE* 4.1 24.9 - - + -
115A GLU* 3.8 33.4 - - + +
149A HIS* 3.6 0.5 - - - -
150A ILE* 2.8 42.1 + - + +
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Residues in contact with LEU 73 (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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38A LEU* 4.2 34.3 - - + -
41A TYR* 6.2 0.2 - - + -
59A VAL 3.4 2.3 - - - +
60A LEU* 3.3 7.3 - - - -
61A VAL* 2.7 54.2 + - + +
62A ARG 5.2 0.2 - - - +
63A ASP* 3.6 34.1 - - + +
71A HIS* 3.9 1.8 - - - +
72A LEU* 1.3 83.9 - - - +
74A LEU* 1.3 59.7 + - - +
75A MET* 4.0 2.5 - - + -
147A HIS* 4.1 19.1 - - + -
148A LEU 3.4 2.7 - - - +
149A HIS* 3.5 33.7 - - + +
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Residues in contact with LEU 74 (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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58A VAL* 3.9 20.9 - - + -
59A VAL 3.6 15.9 - - - +
60A LEU* 4.0 3.6 - - + +
73A LEU* 1.3 71.9 - - - +
75A MET* 1.3 60.8 + - - +
76A THR 4.2 0.9 + - - -
100A LEU* 3.9 49.1 - - + +
103A TYR* 4.2 9.0 - - + -
104A VAL* 3.9 16.6 - - + -
108A LEU* 3.9 22.9 - - + -
146A LEU* 4.2 0.5 - - - +
147A HIS* 3.7 0.9 - - - -
148A LEU* 2.9 46.7 + - + +
150A ILE* 3.8 15.7 - - + +
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Residues in contact with MET 75 (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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38A LEU* 3.5 48.9 - - + +
41A TYR* 4.3 6.5 - - - -
42A ILE* 3.6 25.7 - - + +
58A VAL* 3.2 6.2 - - - -
59A VAL* 2.8 43.6 + - + +
61A VAL* 4.2 18.8 - - - -
73A LEU* 4.5 7.4 - - + +
74A LEU* 1.3 76.3 - - - +
76A THR* 1.3 63.3 + - - +
82A THR* 5.1 0.4 - - - +
100A LEU* 5.3 0.2 - - - -
145A ASN* 3.6 23.8 - - + +
146A LEU 3.6 15.3 - - - +
147A HIS* 3.9 10.3 - - + -
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Residues in contact with THR 76 (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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42A ILE* 3.3 18.7 - - - +
57A ASP 3.6 8.8 + - - -
58A VAL* 4.5 4.9 - - - +
74A LEU 4.2 0.8 + - - -
75A MET* 1.3 74.1 - - - +
77A ARG* 1.3 62.3 + - - +
78A ASP* 3.1 19.7 + - - +
81A LEU* 4.0 5.7 - - + +
82A THR* 3.7 34.4 + - - +
96A LEU* 4.3 22.6 - - - +
100A LEU* 4.9 5.8 - - - +
146A LEU* 3.9 26.5 + - + +
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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