Contacts of the helix formed by residues 88 - 96 (chain H) in PDB entry 3P1M
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 SER 88 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H GLY 3.9 1.2 + - - -
87H ASP* 1.3 75.9 - - - +
89H LEU* 1.3 63.5 + - - +
90H LEU* 3.4 9.5 + - - +
91H ASP* 3.0 50.5 + - - +
92H VAL* 3.0 13.4 + - - +
152H CYS 3.7 22.7 + - - -
154H ILE 3.4 10.8 - - - -
155H CYS* 4.2 11.0 - - - +
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Residues in contact with LEU 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69H VAL* 4.1 7.6 - - + -
71H PHE* 4.0 25.4 - - + -
88H SER* 1.3 70.8 - - - +
90H LEU* 1.3 61.3 + - - +
92H VAL* 3.2 9.2 + - + +
93H VAL* 3.0 27.5 + - - +
103H PHE* 5.1 1.3 - - - -
117H LEU* 4.0 16.6 - - + -
119H PHE* 3.7 23.1 - - + -
151H GLY 3.1 11.4 + - - +
154H ILE* 3.1 44.0 + - + +
156H LEU* 4.2 13.9 - - + -
163H MET* 3.8 24.5 - - + -
165H VAL* 4.8 2.0 - - + -
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Residues in contact with LEU 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H FES 4.0 5.4 - - - -
88H SER* 3.1 5.8 + - - +
89H LEU* 1.3 74.8 - - - +
91H ASP* 1.3 71.3 + - - +
93H VAL* 3.0 4.9 + - + +
94H VAL* 2.9 39.2 + - + +
103H PHE* 3.8 33.2 - - + +
104H GLY* 3.8 15.0 - - - +
107H GLU* 3.9 9.6 - - - +
108H GLY* 3.6 35.2 - - - +
115H CYS* 5.1 0.2 - - + -
151H GLY 3.6 4.9 + - - -
152H CYS* 3.6 22.7 - - + -
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Residues in contact with ASP 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H ASP* 4.0 21.4 - - + +
88H SER* 3.0 45.4 + - - +
90H LEU* 1.3 80.0 - - - +
92H VAL* 1.3 55.2 + - - +
94H VAL* 4.6 4.7 - - - +
95H GLU* 2.7 42.5 + - + +
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Residues in contact with VAL 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H VAL* 5.3 3.4 - - + -
71H PHE* 4.0 15.3 - - + -
81H THR* 3.6 30.1 - - + -
82H LYS 4.8 2.5 - - - +
83H GLY* 4.2 10.8 - - - +
87H ASP* 4.5 7.6 - - + +
88H SER 3.0 13.9 + - - +
89H LEU* 3.4 15.3 - - + +
90H LEU 3.0 0.8 - - - -
91H ASP* 1.3 76.8 - - - +
93H VAL* 1.3 62.5 + - - +
95H GLU* 5.0 1.6 - - - -
96H ASN* 3.1 32.0 + - - +
98H LEU* 4.4 0.3 - - - +
156H LEU* 3.8 28.5 - - + -
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71H PHE* 3.7 27.1 - - + -
89H LEU 3.0 14.5 + - - +
90H LEU 3.0 7.1 + - - +
92H VAL* 1.3 76.5 - - - +
94H VAL* 1.3 61.5 + - + +
96H ASN 3.9 0.2 - - - -
97H ASN* 3.2 20.6 + - - -
98H LEU* 3.2 27.3 + - + +
100H ILE* 3.8 30.7 - - + +
103H PHE* 3.8 35.2 - - + +
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Residues in contact with VAL 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H LEU* 2.9 39.9 + - + +
91H ASP* 4.0 3.8 - - - +
93H VAL* 1.3 76.6 - - + +
95H GLU* 1.3 66.4 + - - +
96H ASN 3.1 2.0 - - - -
97H ASN* 3.0 16.0 + - - +
103H PHE 5.5 3.1 - - - +
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Residues in contact with GLU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H ASP* 5.7 4.3 - - - +
91H ASP* 2.7 26.1 + - + +
92H VAL* 4.6 1.3 - - - +
94H VAL* 1.3 74.8 - - - +
96H ASN* 1.3 67.1 + - - +
97H ASN* 3.9 1.0 + - - +
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Residues in contact with ASN 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81H THR* 3.0 27.9 + - - +
82H LYS 3.0 19.5 + - - +
83H GLY* 5.0 0.2 - - - -
92H VAL* 3.1 25.0 + - - +
93H VAL 3.9 0.2 - - - -
94H VAL 3.1 0.4 - - - -
95H GLU* 1.3 87.3 + - - +
97H ASN* 1.3 69.9 + - - +
98H LEU* 3.3 15.4 + - + +
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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