Contacts of the helix formed by residues 104 - 115 (chain B) in PDB entry 1TLF
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 VAL 104 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B SER 3.8 0.6 + - - -
103B GLY* 1.3 70.9 - - - -
105B GLU* 1.3 58.7 + - + +
107B CYS* 3.2 7.4 - - - +
108B LYS* 2.7 46.5 + - + +
128B LEU* 4.3 4.3 - - - +
132B ASP* 3.2 63.6 + - + +
135B ALA* 4.2 11.0 - - + -
136B VAL* 4.5 5.2 - - + -
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Residues in contact with GLU 105 (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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102B SER 4.1 5.1 + - - +
103B GLY 3.4 0.8 - - - -
104B VAL* 1.3 81.5 - - + +
106B ALA* 1.3 68.9 + - - +
108B LYS* 2.8 45.2 + - - +
109B ALA* 3.1 14.3 + - - +
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Residues in contact with ALA 106 (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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99B VAL* 3.4 20.1 - - + +
100B GLU* 4.2 20.4 - - - +
102B SER* 3.4 45.4 + - - +
103B GLY 3.3 5.0 + - - +
105B GLU* 1.3 79.0 - - - +
107B CYS* 1.3 63.2 + - - +
109B ALA* 3.8 5.2 + - - +
110B ALA* 3.7 14.0 + - - +
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Residues in contact with CYS 107 (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 ALA* 5.8 1.6 - - - -
99B VAL* 3.8 11.4 - - - -
103B GLY 2.9 17.9 + - - +
104B VAL 3.2 8.3 - - - +
106B ALA* 1.3 77.4 - - - +
108B LYS* 1.3 63.2 + - - +
110B ALA* 3.4 7.1 - - - +
111B VAL* 3.3 23.9 + - - +
124B ILE* 4.1 7.0 - - - -
126B TYR* 3.4 25.4 - - + -
128B LEU* 3.3 39.5 - - + -
136B VAL* 3.8 8.7 - - + -
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Residues in contact with LYS 108 (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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104B VAL* 2.7 32.5 + - + +
105B GLU* 2.8 38.1 + - - +
107B CYS* 1.3 73.1 - - - +
109B ALA* 1.3 49.2 + - - +
111B VAL* 2.7 15.0 + - - +
112B HIS* 2.7 34.2 + - - +
135B ALA* 5.2 8.3 - - + +
136B VAL* 4.3 14.4 - - + -
139B ALA* 4.5 19.3 - - + +
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Residues in contact with ALA 109 (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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100B GLU* 4.9 9.4 - - - +
105B GLU 3.1 13.0 + - - +
106B ALA* 4.0 6.7 - - - +
108B LYS* 1.3 75.5 - - - +
110B ALA* 1.3 52.9 + - - +
112B HIS* 3.2 13.3 + - - +
113B ASN* 2.7 41.9 + - - +
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Residues in contact with ALA 110 (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 ALA* 4.0 18.8 - - + -
97B SER* 3.7 18.6 + - - +
98B MET 4.6 7.2 - - - +
99B VAL* 4.1 11.9 - - + -
100B GLU* 5.5 1.3 + - - +
106B ALA 3.7 10.5 + - - +
107B CYS 3.4 11.4 + - - +
108B LYS 3.1 0.2 - - - -
109B ALA* 1.3 73.3 - - - +
111B VAL* 1.3 67.5 + - - +
113B ASN* 2.8 16.6 + - - +
114B LEU* 2.8 18.2 + - - +
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Residues in contact with VAL 111 (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 ALA* 5.0 4.5 - - + -
107B CYS* 3.3 16.8 - - - +
108B LYS* 2.7 14.4 + - - +
110B ALA* 1.3 70.1 - - + +
112B HIS* 1.3 54.2 + - - +
114B LEU* 2.7 32.3 + - + +
115B LEU* 2.8 16.4 + - + +
122B LEU* 3.6 28.0 - - + -
124B ILE* 4.7 9.4 - - + -
136B VAL* 3.5 26.2 - - + -
139B ALA* 4.2 22.9 - - + +
140B CYS* 4.0 11.9 - - - -
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Residues in contact with HIS 112 (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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108B LYS 2.7 15.4 + - - +
109B ALA* 3.3 18.2 + - - +
111B VAL* 1.3 73.1 - - - +
113B ASN* 1.3 72.2 + - - +
115B LEU* 4.1 9.6 - - - +
116B ALA* 3.2 32.9 + - + +
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Residues in contact with ASN 113 (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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63A LEU* 4.5 9.3 - - - +
93A SER* 4.1 24.7 + - - -
94A VAL 5.2 5.3 + - - +
95A VAL* 6.2 0.2 - - - +
118A ARG* 5.9 2.2 - - - +
97B SER* 3.9 14.5 + - - +
109B ALA* 2.7 24.7 + - - +
110B ALA* 2.8 10.4 + - - +
112B HIS* 1.3 83.8 + - - +
114B LEU* 1.3 62.2 + - - +
116B ALA* 3.7 6.9 + - - +
117B GLN* 3.3 32.1 + - - +
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Residues in contact with LEU 114 (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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65B GLY* 3.9 13.0 - - - -
66B VAL 4.1 1.1 - - - +
67B ALA* 3.6 38.6 - - + +
95B VAL* 3.6 30.1 - - + +
97B SER* 3.5 21.1 - - - -
110B ALA 2.8 16.6 + - - +
111B VAL* 2.7 15.2 + - + +
113B ASN* 1.3 71.3 - - - +
115B LEU* 1.3 56.1 + - - +
117B GLN* 2.6 30.1 + - + +
119B VAL* 3.1 15.5 - - + +
122B LEU* 3.5 30.1 - - + -
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Residues in contact with LEU 115 (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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111B VAL* 2.8 30.4 + - + +
112B HIS* 4.1 6.5 - - - +
114B LEU* 1.3 66.0 - - - +
116B ALA* 1.3 53.9 + - - +
117B GLN 2.7 14.0 + - - -
118B ARG* 2.9 17.2 + - - -
119B VAL* 3.8 7.1 + - + +
122B LEU* 3.9 15.9 - - + -
139B ALA 3.2 27.1 - - - +
141B THR* 3.5 29.8 - - + +
143B VAL* 3.8 30.5 - - + -
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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