Contacts of the helix formed by residues 85 - 93 (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 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B HIS 3.7 3.4 + - - -
84B VAL* 1.3 75.6 - - - +
86B PRO* 1.4 82.4 - - + +
87B LEU* 3.1 40.6 + - + +
88B GLU* 2.9 17.5 + - + +
89B ILE* 2.9 19.1 + - - +
139B ALA 3.0 23.8 + - - -
141B PRO* 4.0 4.6 - - + +
187B ARG* 3.2 48.4 + - + +
702B SO4 3.0 27.6 + - - -
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Residues in contact with PRO 86 (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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84B VAL 3.5 3.5 - - - +
85B HIS* 1.4 98.3 - - + +
87B LEU* 1.3 57.8 + - + +
89B ILE* 3.2 3.9 + - + +
90B MET* 2.9 34.3 + - - +
137B PHE* 3.6 32.0 - - + -
138B HIS 3.4 21.5 - - - +
141B PRO* 3.5 20.6 - - + -
146B LEU* 3.7 21.5 - - + -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B HIS* 3.1 21.6 + - + +
86B PRO* 1.3 78.5 - - + +
88B GLU* 1.3 56.9 + - + +
90B MET* 3.4 4.9 + - + +
91B MET* 3.0 42.6 + - + +
139B ALA* 4.0 16.4 - - + +
175B VAL* 4.1 17.5 - - + -
184B LEU* 4.1 13.9 - - + +
185B PRO* 3.5 37.0 - - + +
186B THR 4.0 1.6 - - - +
187B ARG* 3.5 43.3 - - + +
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Residues in contact with GLU 88 (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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84B VAL* 3.6 14.6 - - + -
85B HIS* 2.9 24.0 + - + +
87B LEU* 1.3 75.0 - - + +
89B ILE* 1.3 61.7 + - - +
91B MET* 3.3 26.3 - - + +
92B LYS* 2.9 58.2 + - + +
93B HIS* 3.5 10.5 - - + +
187B ARG* 5.3 6.3 - - - +
176C LYS* 3.6 19.5 - - - +
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Residues in contact with ILE 89 (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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81B LEU* 4.1 6.3 - - + +
84B VAL* 3.5 27.8 - - + +
85B HIS 2.9 16.9 + - - +
86B PRO* 3.4 9.4 - - + +
88B GLU* 1.3 77.0 - - - +
90B MET* 1.3 60.2 + - - +
93B HIS* 2.9 46.9 + - + +
96B LEU* 3.9 32.1 - - + -
97B VAL* 3.8 18.3 - - + +
100B LEU* 5.4 0.4 - - + -
137B PHE* 4.5 11.7 - - + -
146B LEU* 3.8 27.1 - - + -
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Residues in contact with MET 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PRO 2.9 21.4 + - - +
87B LEU* 3.6 4.0 - - + +
89B ILE* 1.3 76.5 - - - +
91B MET* 1.3 60.6 + - - +
94B ARG* 2.8 37.7 + - - +
97B VAL* 4.2 7.6 - - - -
137B PHE* 3.9 17.9 - - + -
175B VAL* 4.3 7.4 - - + -
176B LYS 3.7 16.2 - - - +
177B ILE* 3.6 45.3 - - - +
179B THR 3.9 17.0 - - - +
181B THR* 3.5 4.5 + - - -
184B LEU* 3.6 32.1 - - + -
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Residues in contact with MET 91 (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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87B LEU* 3.0 27.3 + - + +
88B GLU* 3.3 26.9 - - - +
90B MET* 1.3 79.3 - - - +
92B LYS* 1.3 74.2 + - + +
93B HIS 3.8 0.4 - - - -
94B ARG* 4.4 9.2 - - - +
181B THR* 4.3 7.3 + - - +
184B LEU* 3.5 23.3 - - + -
179C THR* 4.8 4.7 - - + -
180C PRO* 4.0 23.2 - - + +
183C ASN* 3.8 38.6 - - - +
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Residues in contact with LYS 92 (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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88B GLU* 2.9 46.8 + - + +
91B MET* 1.3 92.4 - - + +
93B HIS* 1.3 75.3 + - + +
94B ARG* 3.7 4.9 + - - -
703B SO4 5.0 1.7 + - - -
176C LYS* 3.3 19.8 - - - +
178C ASP* 3.0 59.4 + - - +
179C THR* 4.0 9.9 + - - +
180C PRO* 4.5 5.2 - - + -
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Residues in contact with HIS 93 (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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80B HIS* 5.0 7.0 - + - -
81B LEU* 3.7 16.6 - - + +
84B VAL* 4.1 14.9 - - + +
88B GLU* 3.5 19.9 - - + +
89B ILE* 2.9 38.3 + - + +
92B LYS* 1.3 89.7 + - + +
94B ARG* 1.3 63.9 + - - +
96B LEU* 3.1 6.4 + - + +
97B VAL* 3.1 21.8 + - - +
703B SO4 2.7 39.4 + - - +
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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