Contacts of the helix formed by residues 94 - 105 (chain C) in PDB entry 6N1G
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 ASN 94 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92C HIS 3.2 3.2 + - - -
93C MET* 1.3 76.8 - - - +
95C ALA* 1.3 68.0 + - - +
96C ALA* 3.0 17.8 + - - +
97C VAL* 3.3 23.4 - - + +
98C THR* 3.0 23.6 + - - -
119C GLN* 3.4 4.4 - - - +
179C THR* 4.6 2.8 - - - +
182C LEU* 3.9 22.2 - - - +
225C ILE 3.4 12.3 + - - -
226C ASN* 2.5 27.8 + - - +
227C PRO* 3.1 17.5 - - - +
228C SER* 5.7 0.7 - - - -
265C ALA* 5.7 0.2 - - - +
403C GOL 5.3 4.0 - - - +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94C ASN* 1.3 73.4 + - - +
96C ALA* 1.3 55.6 + - - +
98C THR* 4.1 3.1 - - - -
99C PHE* 3.3 19.2 + - - +
112C PHE* 3.5 14.5 - - + -
116C VAL* 3.6 27.6 - - + -
119C GLN* 3.2 14.9 + - - +
226C ASN* 4.8 0.6 - - - +
227C PRO* 3.9 27.3 - - + +
228C SER* 4.7 7.4 - - - +
262C LEU* 4.8 5.3 - - + +
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASN* 3.0 17.0 + - - +
95C ALA* 1.3 76.2 - - - +
97C VAL* 1.3 60.2 + - - +
98C THR 3.2 1.8 - - - -
99C PHE* 3.3 6.7 + - - +
100C ALA* 2.9 30.8 + - - +
179C THR* 4.6 0.2 - - + -
227C PRO* 4.0 5.1 - - + +
261C PRO* 3.6 34.1 - - + +
262C LEU* 3.8 10.1 - - + +
265C ALA* 3.6 13.6 - - + +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ALA 4.7 2.5 - - - +
92C HIS* 3.8 27.9 + - + -
93C MET 4.1 1.8 - - - +
94C ASN* 3.2 34.6 + - + +
96C ALA* 1.3 76.7 - - - +
98C THR* 1.3 61.5 + - - +
100C ALA 3.9 0.2 - - - -
101C ASN* 3.2 27.0 + - - +
182C LEU* 5.6 2.2 - - + -
183C GLN* 3.4 34.0 + - - +
186C LEU* 3.6 32.5 - - + -
187C PHE* 5.3 0.7 - - + -
265C ALA* 5.0 0.2 - - - -
403C GOL 5.5 0.7 - - - +
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Residues in contact with THR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C HIS* 3.1 39.9 + - + +
94C ASN 3.0 16.6 + - - -
95C ALA* 4.1 2.5 - - - -
97C VAL* 1.3 77.2 - - - +
99C PHE* 1.3 63.0 + - - +
101C ASN* 3.3 2.4 + - - +
102C CYS* 2.8 36.0 + - - -
107C VAL* 5.0 0.9 - - + -
112C PHE* 3.4 26.9 - - + -
115C TYR* 3.8 23.5 - - + +
116C VAL* 6.4 0.4 - - - -
119C GLN* 4.3 5.8 + - - -
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Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ALA 3.3 11.8 + - - +
96C ALA* 3.3 7.5 + - - +
98C THR* 1.3 77.6 - - - +
100C ALA* 1.3 59.4 + - + +
102C CYS* 3.8 7.0 + - + +
103C ALA* 3.5 24.5 + - + +
112C PHE* 3.4 40.5 - + + -
262C LEU* 3.8 43.1 - - + -
266C TYR* 5.5 15.0 - + + -
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Residues in contact with ALA 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ALA 2.9 11.9 + - - +
99C PHE* 1.3 75.5 - - + +
101C ASN* 1.3 60.0 + - - +
102C CYS 3.2 1.1 - - - -
103C ALA* 3.9 5.3 - - - +
104C LEU* 3.1 31.7 + - - +
183C GLN* 3.3 30.3 - - + +
187C PHE* 4.3 6.1 - - + -
265C ALA* 3.7 22.0 - - + +
266C TYR* 4.5 8.3 - - + +
269C GLY* 5.4 1.6 - - - -
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Residues in contact with ASN 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C HIS* 3.4 20.7 + - + -
97C VAL* 3.2 21.0 + - + +
98C THR 3.3 3.5 + - - +
100C ALA* 1.3 75.5 - - - +
102C CYS* 1.3 58.0 + - - +
105C GLY* 2.9 42.8 + - - +
107C VAL* 3.1 26.4 + - + +
187C PHE* 4.7 16.9 - - + -
401C GOL 5.1 3.3 + - - -
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Residues in contact with CYS 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C THR* 2.8 32.5 + - - +
99C PHE* 3.9 9.9 - - + +
100C ALA 3.2 0.2 - - - -
101C ASN* 1.3 79.9 - - - +
103C ALA* 1.3 58.4 + - - +
104C LEU 3.4 0.4 + - - -
106C ARG* 3.9 11.3 + - - -
107C VAL* 3.3 41.3 + - - +
108C PRO 4.4 2.5 - - - -
109C TRP* 5.1 5.2 - - + -
112C PHE* 3.9 27.8 - - - -
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Residues in contact with ALA 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C PHE* 3.5 20.9 + - + +
100C ALA* 3.7 2.9 + - - +
102C CYS* 1.3 78.6 - - - +
104C LEU* 1.3 61.8 + - + +
106C ARG 5.2 0.4 - - - -
266C TYR* 4.0 30.5 - - + -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ALA 3.1 14.8 + - - +
101C ASN* 4.8 0.2 - - - -
103C ALA* 1.3 79.1 - - + +
105C GLY* 1.3 57.8 + - - +
106C ARG 3.8 1.6 - - - -
187C PHE* 3.5 27.6 - - + -
266C TYR* 6.3 2.0 - - + -
269C GLY* 3.1 32.8 - - - +
270C ILE* 4.6 11.9 - - + -
273C LEU* 3.5 40.2 - - + +
401C GOL 3.8 24.8 - - - +
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Residues in contact with GLY 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASN* 2.9 34.7 + - - +
104C LEU* 1.3 79.3 - - - +
106C ARG* 1.3 85.5 + - - +
107C VAL* 3.0 4.2 + - - +
187C PHE* 6.3 0.2 - - - -
401C GOL 4.6 12.1 - - - -
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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