Contacts of the helix formed by residues 140 - 156 (chain I) in PDB entry 3DLQ
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 140 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82I GLY 3.5 24.9 + - - -
83I VAL* 4.5 2.2 - - + -
87I GLU* 3.2 32.9 + - - -
141I ILE* 1.3 96.5 + - + +
142I GLN* 3.2 7.5 - - - +
143I ARG* 3.1 47.1 + - - +
144I ASN* 3.2 18.1 + - - +
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Residues in contact with ILE 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I VAL* 3.7 29.6 - - + -
87I GLU* 4.4 11.7 - - + +
90I TYR* 4.0 33.2 - - + -
91I LEU* 4.0 30.7 - - + -
94I GLN* 4.4 4.7 - - + -
140I HIS* 1.3 104.4 - - + +
142I GLN* 1.3 67.1 + - + +
143I ARG 3.2 0.3 + - - -
144I ASN* 3.2 4.0 + - - +
145I VAL* 3.1 27.6 + - + +
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Residues in contact with GLN 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I GLN* 6.0 3.6 - - - +
140I HIS 3.2 4.6 - - - +
141I ILE* 1.3 80.3 - - + +
143I ARG* 1.3 57.0 + - - +
145I VAL* 3.9 5.6 - - - +
146I GLN* 2.9 33.5 + - - +
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Residues in contact with ARG 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81I HIS 4.3 11.7 + - - -
82I GLY* 4.8 8.1 + - - -
140I HIS* 3.1 37.9 + - - +
141I ILE 3.1 0.4 - - - -
142I GLN* 1.3 81.0 - - - +
144I ASN* 1.3 76.6 + - - +
146I GLN* 3.3 5.6 + - - +
147I LYS* 3.2 20.3 + - - +
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Residues in contact with ASN 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I LYS 3.9 5.1 + - - -
79I LEU* 2.9 46.1 + - + +
81I HIS* 2.8 28.6 + - - +
83I VAL* 3.4 12.9 - - - +
91I LEU* 4.2 6.5 - - + -
140I HIS 3.2 7.1 + - - +
141I ILE 3.2 6.1 + - - +
143I ARG* 1.3 96.5 + - - +
145I VAL* 1.3 65.3 + - - +
147I LYS* 3.3 15.1 + - - +
148I LEU 3.4 8.8 + - - -
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Residues in contact with VAL 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I LEU* 4.8 2.5 - - - -
91I LEU* 4.4 13.7 - - + +
94I GLN* 3.9 39.0 - - + +
95I VAL* 4.4 11.0 - - + +
98I PHE* 5.1 2.7 - - + -
141I ILE* 3.1 25.8 + - + +
142I GLN* 3.9 5.8 - - - +
144I ASN* 1.3 74.6 - - - +
146I GLN* 1.3 66.2 + - - +
148I LEU* 3.2 9.7 + - + +
149I LYS* 3.0 44.5 + - + +
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Residues in contact with GLN 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142I GLN 2.9 19.4 + - - +
143I ARG* 3.7 6.7 - - - +
144I ASN 3.2 0.2 - - - -
145I VAL* 1.3 75.7 - - - +
147I LYS* 1.3 58.8 + - - +
149I LYS* 3.1 28.5 + - - +
150I ASP* 2.8 63.3 + - - +
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Residues in contact with LYS 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I LYS* 5.9 9.6 - - + +
143I ARG 3.2 12.5 + - - +
144I ASN* 3.6 11.2 - - - +
145I VAL 3.1 0.8 - - - -
146I GLN* 1.3 77.1 - - - +
148I LEU* 1.3 60.5 + - - +
150I ASP* 3.2 18.9 + - + +
151I THR* 3.0 33.0 + - - +
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Residues in contact with LEU 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I LEU* 3.8 33.7 - - + +
75I ILE* 3.9 20.9 - - + -
79I LEU* 4.2 22.0 - - + -
95I VAL* 4.6 14.4 - - + -
98I PHE* 3.5 33.2 - - + -
99I THR* 5.7 0.9 - - - +
144I ASN 3.4 8.8 + - - +
145I VAL* 3.2 11.5 + - + +
147I LYS* 1.3 79.9 - - - +
149I LYS* 1.3 62.0 + - + +
151I THR* 3.2 6.2 + - - -
152I VAL* 3.0 28.1 + - + +
163I ALA* 6.0 1.3 - - + -
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Residues in contact with LYS 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94I GLN 5.7 0.2 - - - -
98I PHE* 3.7 50.6 - - + +
102I GLU* 4.3 12.0 + - - +
145I VAL* 3.0 37.5 + - + +
146I GLN* 3.4 30.5 + - - +
148I LEU* 1.3 76.3 - - - +
150I ASP* 1.3 63.0 + - - +
152I VAL* 3.3 3.1 + - - +
153I LYS* 3.0 25.8 + - - +
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Residues in contact with ASP 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I GLN* 2.8 50.6 + - - +
147I LYS* 3.2 22.4 + - + +
149I LYS* 1.3 72.7 - - - +
151I THR* 1.3 58.2 + - - +
153I LYS* 3.4 6.6 + - - +
154I LYS* 2.8 30.8 + - - +
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Residues in contact with THR 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72I VAL* 4.0 17.9 - - + -
73I ARG 5.9 0.2 - - - +
74I LEU* 3.5 26.0 - - + -
147I LYS* 3.0 23.9 + - - +
148I LEU* 3.7 6.0 - - - -
150I ASP* 1.3 75.2 - - - +
152I VAL* 1.3 66.4 + - - +
154I LYS* 3.3 10.5 + - + +
155I LEU* 3.1 28.0 + - + +
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Residues in contact with VAL 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74I LEU* 3.8 29.4 - - + -
98I PHE* 4.1 19.3 - - + -
102I GLU 5.9 0.2 - - - +
103I VAL* 4.7 3.1 - - + -
148I LEU* 3.0 30.2 + - + +
149I LYS 3.7 6.7 - - - +
151I THR* 1.3 77.2 - - - +
153I LYS* 1.3 61.3 + - + +
155I LEU 3.3 1.6 + - - -
156I GLY 3.3 22.2 + - - +
159I GLY* 3.7 28.0 - - - +
160I GLU* 3.9 17.3 - - + +
163I ALA* 4.6 4.3 - - + -
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Residues in contact with LYS 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I GLU* 5.0 10.2 + - - +
149I LYS 3.0 16.9 + - - +
150I ASP* 3.5 7.4 - - - +
152I VAL* 1.3 76.2 - - + +
154I LYS* 1.3 66.0 + - - +
156I GLY* 3.0 15.1 + - - -
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Residues in contact with LYS 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I ASP 2.8 20.9 + - - +
151I THR* 3.3 11.0 + - + +
153I LYS* 1.3 73.3 - - - +
155I LEU* 1.3 68.2 + - + +
156I GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I ASN* 3.4 23.1 - - + +
72I VAL* 4.1 19.1 - - + -
74I LEU* 4.6 1.8 - - + -
151I THR* 3.1 24.0 + - + +
152I VAL 3.3 0.2 + - - -
153I LYS 3.2 0.2 - - - -
154I LYS* 1.3 83.4 - - + +
156I GLY* 1.3 61.2 + - - +
158I SER* 3.7 18.7 + - - +
159I GLY* 3.5 23.1 - - - +
162I LYS* 3.7 36.3 - - + -
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Residues in contact with GLY 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I VAL 3.3 6.1 + - - +
153I LYS* 3.0 16.7 + - - -
154I LYS 3.2 1.6 + - - -
155I LEU* 1.3 73.8 - - - +
157I GLU* 1.3 62.5 + - - -
158I SER 3.1 2.7 - - - -
159I GLY* 2.8 22.2 + - - -
160I GLU* 3.5 7.5 + - - +
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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