Contacts of the strand formed by residues 71 - 76 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62D ARG* 3.9 1.7 - - - +
63D ASP* 3.0 47.3 + - + +
66D PRO* 3.6 24.7 - - + +
67D LYS* 2.9 30.4 + - + +
68D SER 4.2 2.6 + - - +
69D LYS 4.2 0.4 + - - -
70D MET* 1.3 76.7 - - - +
72D LEU* 1.3 78.2 + - - +
73D LEU* 3.9 0.2 - - - +
115D GLU* 5.5 0.8 + - - -
149D HIS* 2.9 25.2 + + + -
150D ILE 3.7 2.9 - - - -
151D MET* 3.7 20.5 - - + +
169D PHE* 3.7 24.9 - + - -
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Residues in contact with LEU 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D ILE* 4.0 19.3 - - + -
60D LEU* 4.0 14.6 - - + -
61D VAL 3.4 5.6 - - - +
62D ARG* 3.9 19.1 - - + -
70D MET* 4.0 27.6 - - + -
71D HIS* 1.3 83.1 - - - +
73D LEU* 1.3 70.8 + - - +
112D ILE* 4.1 23.8 - - + -
115D GLU* 3.8 31.4 - - + +
149D HIS* 3.5 0.7 - - - -
150D ILE* 2.8 40.5 + - + +
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Residues in contact with LEU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 4.1 33.9 - - + -
41D TYR* 6.2 0.7 - - + -
59D VAL 3.5 2.1 - - - +
60D LEU* 3.3 7.0 - - - +
61D VAL* 2.8 52.7 + - + +
62D ARG 5.3 0.2 - - - +
63D ASP* 3.7 33.9 - - + +
71D HIS* 3.9 2.2 - - - +
72D LEU* 1.3 85.0 - - - +
74D LEU* 1.3 59.3 + - - +
75D MET* 4.4 2.7 - - + -
147D HIS* 4.1 19.7 - - + -
148D LEU 3.4 2.7 - - - +
149D HIS* 3.5 33.2 - - + +
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Residues in contact with LEU 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D VAL* 4.0 17.3 - - + -
59D VAL 3.4 20.2 - - - +
60D LEU* 4.0 4.9 - - + +
73D LEU* 1.3 71.5 - - - +
75D MET* 1.3 59.5 + - - +
76D THR 4.2 0.9 + - - -
100D LEU* 3.9 49.1 - - + +
103D TYR* 4.2 9.2 - - + -
104D VAL* 4.0 16.2 - - + -
108D LEU* 3.8 23.3 - - + -
137D PHE* 5.5 0.3 - - - -
146D LEU* 4.2 0.7 - - - +
147D HIS* 3.7 0.5 - - - -
148D LEU* 2.8 43.9 + - + +
150D ILE* 3.7 15.9 - - + +
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Residues in contact with MET 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D LEU* 3.5 47.8 - - + +
41D TYR* 4.4 6.7 - - - -
42D ILE* 3.7 23.3 - - + +
58D VAL* 3.2 6.5 - - - -
59D VAL* 2.8 44.7 + - + +
61D VAL* 4.2 19.1 - - - -
73D LEU* 4.4 7.2 - - + +
74D LEU* 1.3 78.2 - - - +
76D THR* 1.3 62.6 + - - +
82D THR* 5.2 0.4 - - - +
100D LEU* 5.4 0.2 - - - -
145D ASN* 3.6 29.2 - - + +
146D LEU 3.6 12.1 - - - +
147D HIS* 3.9 10.1 - - + -
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 3.3 18.5 - - - +
57D ASP 3.6 9.9 + - - -
58D VAL* 4.4 4.7 - - - +
74D LEU 4.2 1.4 + - - -
75D MET* 1.3 74.9 - - - +
77D ARG* 1.3 61.1 + - - +
78D ASP* 3.1 19.5 + - - +
81D LEU* 4.0 6.7 - - + +
82D THR* 3.7 34.1 + - - +
96D LEU* 4.3 22.5 - - - +
100D LEU* 5.0 5.0 - - - +
146D LEU* 3.8 25.9 + - + +
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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