Contacts of the helix formed by residues 101 - 113 (chain B) in PDB entry 3LMK
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 HIS 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A LEU* 5.9 5.2 - - + +
46B GLN* 3.9 18.8 - - - -
47B PRO* 3.7 30.6 - - + +
52B VAL* 4.6 25.2 - - + +
55B ARG* 5.2 0.7 - - + -
98B SER 3.0 8.6 + - - +
99B CYS 3.4 11.0 - - - +
100B TRP* 1.3 77.9 - - - +
102B SER* 1.3 61.6 + - - +
103B ALA* 3.5 28.8 + - + -
104B VAL* 3.6 17.0 + - + +
105B ALA* 2.9 30.0 + - - +
154B VAL* 4.0 7.3 - - - +
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Residues in contact with SER 102 (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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160A ASN* 6.4 1.6 - - - -
101B HIS* 1.3 75.4 - - - +
103B ALA* 1.3 65.5 + - - +
105B ALA* 4.0 0.7 - - - +
106B LEU* 3.0 26.3 + - - +
153B SER* 3.8 9.9 + - - -
154B VAL* 3.7 30.5 + - - +
157B GLN* 4.1 19.4 - - - +
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Residues in contact with ALA 103 (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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160A ASN 5.8 0.9 - - - -
163A GLN* 4.1 19.7 - - - +
164A LEU* 3.9 8.8 - - + +
55B ARG* 3.5 24.0 - - + -
101B HIS* 3.5 19.2 + - + -
102B SER* 1.3 77.4 - - - +
104B VAL* 1.3 59.0 + - - +
106B LEU* 3.3 5.7 + - - +
107B GLU* 2.9 31.2 + - - +
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Residues in contact with VAL 104 (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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26B ARG* 4.0 17.7 - - - +
47B PRO* 4.6 1.8 - - + -
55B ARG* 3.8 29.4 - - + +
57B CYS* 4.1 16.2 - - - -
97B ASP 3.4 22.9 - - - +
98B SER 3.4 15.3 - - - +
99B CYS* 3.7 11.9 - - - -
101B HIS* 3.4 19.3 + - + +
102B SER 3.3 0.2 - - - -
103B ALA* 1.3 77.3 - - - +
105B ALA* 1.3 56.2 + - - +
107B GLU* 3.4 6.9 + - - +
108B GLN* 2.9 28.8 + - + +
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Residues in contact with ALA 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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40B LEU* 4.2 5.9 - - + +
98B SER* 3.9 17.4 + - - +
101B HIS 2.9 19.3 + - - +
102B SER 4.1 2.0 - - - +
104B VAL* 1.3 74.5 - - - +
106B LEU* 1.3 54.4 + - - +
108B GLN* 3.3 5.9 + - - +
109B SER* 2.7 40.2 + - - -
154B VAL* 3.4 24.0 - - + -
157B GLN* 6.3 0.2 - - + -
158B VAL* 3.8 13.9 - - + -
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Residues in contact with LEU 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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106A LEU* 5.9 3.8 - - + -
157A GLN* 5.4 0.4 - - - +
160A ASN* 3.4 35.2 - - + +
161A LEU* 4.1 9.2 - - + +
164A LEU* 3.9 10.3 - - + -
102B SER 3.0 19.3 + - - +
103B ALA* 3.7 4.5 - - - +
105B ALA* 1.3 73.1 - - - +
107B GLU* 1.3 68.1 + - - +
109B SER* 3.0 4.9 + - - -
110B ILE* 2.8 30.5 + - + +
157B GLN* 3.7 36.8 - - + +
158B VAL* 4.8 2.6 - - - +
161B LEU* 4.0 37.0 - - + -
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Residues in contact with GLU 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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164A LEU* 3.6 21.9 - - + +
26B ARG* 3.4 26.8 + - - +
54B GLU 5.5 0.3 - - - +
55B ARG* 2.9 35.9 + - - +
103B ALA 2.9 17.1 + - - +
104B VAL* 3.4 5.0 - - - +
106B LEU* 1.3 76.6 - - - +
108B GLN* 1.3 85.3 + - - +
110B ILE* 3.3 17.9 + - + +
111B GLU* 3.5 11.6 + - + +
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Residues in contact with GLN 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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26B ARG* 3.8 30.8 - - - +
27B VAL 4.8 1.2 - - - +
28B VAL* 4.8 1.7 - - - +
40B LEU* 4.1 13.2 - - + -
96B ARG* 3.0 53.8 + - + +
97B ASP 3.5 21.0 + - - +
104B VAL 2.9 21.0 + - - +
105B ALA 3.8 3.6 - - - +
107B GLU* 1.3 102.7 + - - +
109B SER* 1.3 55.8 + - - +
111B GLU* 3.0 29.4 + - - +
112B PHE* 3.4 6.0 + - - -
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Residues in contact with SER 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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40B LEU* 3.8 8.7 - - - +
105B ALA 2.7 25.3 + - - -
106B LEU* 3.0 9.2 + - - -
108B GLN* 1.3 70.0 - - - +
110B ILE* 1.3 65.8 + - - +
112B PHE* 3.0 31.0 + - - +
113B ILE* 3.4 9.5 + - - +
158B VAL* 3.6 30.2 - - - +
161B LEU* 3.6 18.1 - - - +
162B LEU* 4.7 5.3 - - - +
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Residues in contact with ILE 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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113A ILE* 5.4 5.8 - - + -
161A LEU* 3.8 15.7 - - + -
164A LEU* 3.7 26.0 - - + -
165A PHE* 3.7 39.0 - - + -
106B LEU* 2.8 15.5 + - + +
107B GLU* 3.4 9.0 - - + +
108B GLN 3.3 0.4 - - - -
109B SER* 1.3 75.0 - - - +
111B GLU* 1.3 66.8 + - - +
113B ILE* 3.0 35.3 + - + +
114B ARG* 3.4 16.2 - - + +
161B LEU* 3.7 13.0 - - + +
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Residues in contact with GLU 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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94B GLU* 4.1 8.9 - - - +
96B ARG* 3.4 34.7 + - - +
107B GLU* 3.9 14.5 - - + +
108B GLN* 3.0 20.1 + - - +
110B ILE* 1.3 82.1 - - - +
112B PHE* 1.3 59.7 + - - +
114B ARG* 3.5 42.2 + - - +
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Residues in contact with PHE 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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38B GLY* 3.8 7.9 - - - -
39B ALA 3.5 30.3 - - - -
40B LEU* 3.9 27.6 - - + -
94B GLU* 3.5 31.0 - - + -
96B ARG* 3.8 20.0 - - + -
108B GLN 3.4 1.7 + - - -
109B SER* 3.0 29.0 + - - +
111B GLU* 1.3 80.3 - - - +
113B ILE* 1.3 62.5 + - + +
114B ARG 3.6 3.0 + - - -
115B ASP 4.7 4.7 - - - +
143B ILE* 3.5 47.4 + - + +
146B VAL* 3.9 19.7 - - + -
162B LEU* 5.0 5.6 - - + -
167B ILE* 5.3 0.7 - - - +
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Residues in contact with ILE 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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110A ILE* 5.3 8.5 - - + -
113A ILE* 6.3 1.8 - - + -
109B SER 3.5 11.7 - - - +
110B ILE* 3.0 28.6 + - + +
112B PHE* 1.3 80.4 - - - +
114B ARG* 1.3 56.9 + - + +
115B ASP* 3.4 22.7 - - - +
161B LEU* 4.0 14.8 - - + -
162B LEU* 4.3 11.9 - - + -
165B PHE* 3.8 48.9 - - + -
167B ILE* 3.8 24.0 - - + -
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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