Contacts of the helix formed by residues 92 - 103 (chain C) in PDB entry 6T2C
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 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571B ARG* 5.8 0.7 + - - -
54C LYS 3.9 13.1 + - - -
55C TYR* 3.8 6.0 - - - -
57C ILE* 4.3 4.0 - - - +
75C ASN* 5.7 0.2 - - - +
76C THR 3.6 22.6 + - - -
77C LEU* 3.5 7.5 + - - -
91C VAL* 1.3 77.8 - - - +
93C PRO* 1.3 69.9 - - - +
94C ASN* 3.1 28.4 + - - +
95C ALA* 3.1 24.6 + - - +
96C VAL* 4.1 0.9 + - - +
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Residues in contact with PRO 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLU* 5.5 0.7 - - - +
571B ARG* 5.0 12.1 - - - +
572B ARG* 3.7 36.3 + - + +
666B TRP* 6.3 0.2 - - + -
51C MET* 4.2 14.8 - - + -
54C LYS 4.3 2.7 - - - +
56C PRO* 3.7 24.7 - - + -
57C ILE* 3.8 23.1 - - + -
92C SER* 1.3 87.1 - - - +
94C ASN* 1.3 60.6 + - - +
95C ALA 3.1 0.2 - - - -
96C VAL* 2.9 21.9 + - + +
97C THR* 3.1 16.6 + - - -
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Residues in contact with ASN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B ARG* 2.6 39.5 + - - +
572B ARG* 3.8 13.6 - - - +
574B LYS* 5.1 0.2 - - - +
575B SER* 3.9 18.9 + - - +
71C ASP* 3.7 17.0 - - - +
75C ASN* 3.8 20.4 + - + +
77C LEU* 3.7 7.9 - - + +
92C SER* 3.1 17.7 + - - +
93C PRO* 1.3 77.9 - - - +
95C ALA* 1.3 56.9 + - - +
97C THR* 3.8 7.1 - - - -
98C TRP* 2.8 30.5 + - - +
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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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631B PHE* 4.2 15.4 - - + -
63C ILE* 4.8 1.8 - - + -
67C ILE* 3.8 28.3 - - + +
77C LEU* 3.5 23.8 - - + +
78C TRP* 6.2 0.2 - - + -
91C VAL* 4.4 8.1 - - + -
92C SER 3.1 15.8 + - - +
94C ASN* 1.3 78.0 - - - +
96C VAL* 1.3 56.4 + - - +
98C TRP* 3.3 2.1 + - - +
99C TRP* 2.9 28.6 + - - +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B GLU* 5.8 0.7 - - - +
572B ARG* 5.3 3.1 - - - +
631B PHE* 3.9 28.7 - - + -
663B THR* 4.0 21.5 - - - +
664B HIS* 4.1 22.7 - - + +
666B TRP* 4.1 14.1 - - + +
57C ILE* 4.0 25.1 - - + -
92C SER 4.6 1.1 - - - +
93C PRO* 2.9 12.7 + - + +
95C ALA* 1.3 76.6 - - - +
97C THR* 1.3 57.5 + - - +
99C TRP* 3.3 2.8 + - - +
100C ASN* 2.9 41.9 + - - +
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Residues in contact with THR 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572B ARG* 3.3 24.5 + - - +
575B SER* 3.7 41.5 - - - +
576B ILE* 3.9 13.1 - - + +
579B LEU* 4.0 16.8 - - + -
593B ASP* 4.5 5.8 - - - +
93C PRO 3.1 13.3 + - - -
94C ASN* 3.5 4.6 + - - -
95C ALA 3.4 0.2 - - - -
96C VAL* 1.3 77.1 - - - +
98C TRP* 1.3 57.3 + - - +
100C ASN* 3.2 6.2 + - - +
101C ARG* 3.0 29.0 + - - +
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Residues in contact with TRP 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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575B SER* 4.8 1.5 - - - +
66C MET 4.3 10.3 - - - -
67C ILE* 4.0 28.7 - - + -
68C PRO* 4.1 25.3 - - + +
70C LYS 5.8 0.2 + - - -
71C ASP* 3.5 19.8 + - - +
72C GLU* 3.1 23.0 + - - -
77C LEU* 4.5 3.6 - - + +
94C ASN 2.8 19.1 + - - +
95C ALA* 3.5 8.3 - - - +
96C VAL 3.2 0.2 - - - -
97C THR* 1.3 74.1 - - - +
99C TRP* 1.3 71.6 + + + +
101C ARG* 3.4 31.7 - - - +
102C ALA* 2.9 55.8 + - + +
103C GLY* 5.0 2.5 - - - -
104C PRO* 6.0 1.1 - - + -
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Residues in contact with TRP 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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623B ARG* 3.4 27.1 + - - +
626B ASN* 4.5 11.9 - - - +
628B ASN* 4.4 4.3 - - + -
629B ASN* 3.6 33.4 - - + +
630B PRO* 4.3 4.9 - - + -
631B PHE* 4.2 19.7 - + + -
663B THR* 3.8 16.4 - - + +
63C ILE* 6.0 0.4 - - + -
66C MET* 3.8 44.0 - - + -
67C ILE* 4.8 15.7 - - + -
95C ALA 2.9 16.0 + - - +
96C VAL 3.3 5.1 + - - +
98C TRP* 1.3 84.9 - + - +
100C ASN* 1.3 61.5 + - - +
103C GLY* 3.0 23.1 + - - +
104C PRO* 3.6 39.9 - - + +
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Residues in contact with ASN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B LEU* 4.2 5.6 - - + +
593B ASP* 2.6 42.8 + - - +
620B TYR* 4.0 17.9 - - + +
623B ARG* 3.6 21.1 - - - +
624B LEU* 3.4 21.2 - - - +
663B THR* 2.8 24.3 + - - +
664B HIS* 3.2 14.7 + - - -
96C VAL* 2.9 25.4 + - - +
97C THR 3.2 5.3 + - - +
99C TRP* 1.3 80.5 - - - +
101C ARG* 1.3 58.6 + - - +
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Residues in contact with ARG 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B SER* 3.8 32.5 + - - -
578B ARG* 4.0 39.8 - - - +
579B LEU* 3.8 28.9 - - + +
582B GLU* 4.6 21.0 + - - +
623B ARG* 3.5 16.6 + - - +
71C ASP* 4.7 1.0 + - - -
72C GLU* 2.4 38.0 + - - -
73C ASP* 4.5 1.8 + - - -
97C THR 3.0 17.2 + - - +
98C TRP* 3.4 25.2 - - - +
100C ASN* 1.3 79.7 - - - +
102C ALA* 1.3 71.3 + - + +
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Residues in contact with ALA 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623B ARG* 3.6 8.1 - - - +
98C TRP* 2.9 45.1 + - + +
101C ARG* 1.3 94.8 - - + +
103C GLY* 1.3 64.5 + - - +
104C PRO* 4.7 0.3 - - - +
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Residues in contact with GLY 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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623B ARG* 3.0 29.3 + - - +
98C TRP* 5.0 2.0 - - - -
99C TRP* 3.0 29.2 + - - -
102C ALA* 1.3 79.4 - - - +
104C PRO* 1.3 74.2 - - - +
105C VAL* 3.4 2.3 + - - +
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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