Contacts of the helix formed by residues 95 - 101 (chain B) in PDB entry 3K75
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B SER* 5.1 2.2 + - - -
94B MET* 1.3 72.8 - - - +
96B PRO* 1.3 68.5 - - - +
97B SER* 3.2 8.5 + - - -
98B GLU* 3.0 40.7 + - - +
99B SER* 2.5 37.5 + - - -
136B TYR* 5.0 0.4 - - - -
322D TYR* 5.4 4.9 - - - -
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Residues in contact with PRO 96 (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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67B PHE* 6.1 0.2 - - + -
94B MET 4.5 1.1 - - - +
95B SER* 1.3 90.7 - - - +
97B SER* 1.3 57.1 + - - +
99B SER* 3.4 0.7 + - - -
100B ARG* 2.8 42.1 + - - +
136B TYR* 3.6 46.8 - - + +
318D ASP 5.2 0.7 - - - +
321D ASP* 4.1 18.4 - - + -
322D TYR* 3.9 36.6 - - + +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 3.2 7.0 + - - -
96B PRO* 1.3 76.6 - - - +
98B GLU* 1.3 67.2 + - - +
100B ARG* 3.4 30.8 + - - +
101B SER* 3.2 23.8 + - - -
321D ASP* 4.6 7.1 + - - -
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Residues in contact with GLU 98 (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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94B MET* 3.8 7.0 - - + +
95B SER* 3.0 34.4 + - - +
97B SER* 1.3 76.4 - - - +
99B SER* 1.3 55.9 + - - +
101B SER* 3.1 7.0 + - - -
102B GLY* 2.8 30.8 + - - -
103B SER* 2.9 38.9 + - - +
104B ASN* 4.4 9.0 + - + +
107B ARG* 3.4 33.9 + - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ALA* 4.0 2.3 - - - +
94B MET* 3.4 24.8 + - - +
95B SER 2.5 23.5 + - - -
96B PRO 3.6 4.3 - - - -
97B SER 3.2 0.2 - - - -
98B GLU* 1.3 74.6 - - - +
100B ARG* 1.3 62.3 + - - +
101B SER 3.0 6.1 + - - -
102B GLY* 3.4 8.7 + - - -
134B GLN* 3.1 36.8 + - - +
136B TYR* 3.8 11.2 - - - -
137B SER* 3.7 15.3 - - - -
140B SER* 4.4 5.0 + - - -
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Residues in contact with ARG 100 (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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96B PRO* 2.8 27.7 + - - +
97B SER* 3.8 37.3 + - - +
98B GLU 3.3 0.2 - - - -
99B SER* 1.3 75.4 - - - +
101B SER* 1.3 57.3 + - - +
102B GLY 3.7 0.2 - - - -
136B TYR* 3.3 28.5 - - + +
137B SER* 4.7 2.4 + - - -
140B SER* 5.8 0.9 - - - -
321D ASP* 4.4 19.4 + - - -
324D GLN* 6.1 2.2 - - - +
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Residues in contact with SER 101 (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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97B SER 3.2 15.2 + - - -
98B GLU* 3.1 3.9 + - - -
99B SER 3.0 0.4 - - - -
100B ARG* 1.3 82.2 - - - +
102B GLY* 1.3 64.0 + - - +
103B SER* 2.7 22.8 + - - -
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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