Contacts of the helix formed by residues 95 - 103 (chain A) in PDB entry 1TKP
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA* 1.3 77.3 - - - +
96A PRO* 1.3 71.3 - - - +
97A GLU* 3.7 4.5 + - - +
98A THR* 3.0 28.6 + - - -
99A LEU* 3.0 17.7 + - - +
46B HIS* 4.9 1.3 - - - -
100B GLN* 3.4 14.3 + - - -
107B VAL* 3.8 20.0 - - - -
108B GLU 4.6 4.9 - - - -
110B GLU* 2.7 17.8 + - - +
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Residues in contact with PRO 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A ALA 4.5 0.7 - - - +
95A SER* 1.3 83.9 - - - +
97A GLU* 1.3 61.9 + - - +
99A LEU* 4.4 7.0 - - + -
100A GLN* 2.9 22.0 + - - +
42B TYR 4.6 0.7 - - - +
43B VAL* 4.5 23.1 - - + +
46B HIS* 3.4 36.1 - - + -
96B PRO* 3.3 43.9 - - + +
99B LEU* 5.1 3.4 - - + -
100B GLN* 3.3 18.2 - - + +
107B VAL* 5.0 2.2 - - + -
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Residues in contact with GLU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A SER* 4.0 3.6 + - - +
96A PRO* 1.3 80.5 - - - +
98A THR* 1.3 60.3 + - - +
100A GLN* 4.0 1.6 - - - +
101A ALA* 2.8 35.8 + - + +
97B GLU* 4.9 13.0 - - + +
100B GLN* 3.0 39.1 + - + +
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Residues in contact with THR 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS* 3.6 27.6 - - + +
95A SER* 3.0 20.7 + - - -
97A GLU* 1.3 80.8 + - - +
99A LEU* 1.3 62.3 + - - +
101A ALA* 3.3 5.6 + - - -
102A GLU* 2.8 36.4 + - + +
110B GLU* 3.0 38.9 - - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.0 14.6 - - + +
39A ALA* 3.2 32.4 - - - +
42A TYR* 3.6 20.0 - - + -
43A VAL* 4.4 3.1 - - + -
46A HIS* 6.1 0.2 - - + -
93A HIS* 3.6 31.0 - - + +
94A ALA 3.5 20.9 - - - +
95A SER 3.0 12.4 + - - +
96A PRO* 3.2 6.3 + - + +
98A THR* 1.3 82.0 - - - +
100A GLN* 1.3 63.3 + - - +
103A ALA* 3.1 18.7 + - - +
46B HIS* 3.6 29.2 - - + +
53B TRP* 5.9 0.2 - - + -
96B PRO* 5.1 4.7 - - + -
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Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 3.8 12.9 - - + +
96A PRO 2.9 16.4 + - - +
97A GLU 4.1 2.0 - - - +
99A LEU* 1.3 72.6 - - - +
101A ALA* 1.3 67.6 + - - +
103A ALA* 2.9 18.1 + - + +
107A VAL* 3.3 38.6 - - + +
95B SER* 3.3 6.4 + - - -
96B PRO* 3.2 21.8 - - + +
97B GLU* 3.1 49.7 + - + +
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A GLU* 2.8 28.1 + - + +
98A THR* 3.3 5.8 + - - +
100A GLN* 1.3 75.6 - - - +
102A GLU* 1.4 64.5 + - + +
103A ALA 3.5 4.5 + - - +
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Residues in contact with GLU 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ASN 5.4 0.2 - - - +
36A ALA* 4.7 10.0 - - - +
39A ALA* 3.7 10.5 - - + +
93A HIS* 3.6 45.4 + - + +
98A THR* 2.8 26.2 + - + +
101A ALA* 1.4 79.3 - - + +
103A ALA* 1.3 63.5 + - - +
104A SER* 3.6 2.3 + - - -
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ALA* 3.9 8.3 - - - +
40A ASN* 3.3 14.4 - - - +
43A VAL* 3.5 29.2 - - + -
99A LEU 3.1 6.1 + - - +
100A GLN* 2.9 17.9 + - + +
101A ALA 3.9 4.3 - - - +
102A GLU* 1.3 79.8 - - - +
104A SER* 1.3 62.0 + - - +
105A VAL* 3.8 11.5 + - + +
107A VAL* 6.0 0.7 - - + -
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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