Contacts of the helix formed by residues 135 - 143 (chain H) in PDB entry 1XBT
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 ALA 135 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100H GLN 5.0 2.8 + - - -
102H PHE 5.5 1.7 + - - +
103H PRO* 4.9 10.5 - - + +
105H ILE* 4.4 12.6 - - + +
106H VAL* 3.7 16.2 - - + +
107H GLU* 5.9 0.9 - - - +
133H PHE 3.5 0.4 + - - -
134H GLY* 1.3 71.3 - - - -
136H ILE* 1.3 64.6 + - - +
137H LEU 3.3 2.9 - - - -
138H ASN* 3.0 37.6 + - - +
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Residues in contact with ILE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H VAL* 4.7 9.7 - - + +
25H LEU* 4.4 7.6 - - + +
99H GLY 3.9 5.2 - - - +
100H GLN* 3.8 19.2 - - - +
105H ILE* 4.6 7.7 - - + +
121H VAL* 4.2 7.0 - - + -
123H ALA* 3.5 28.5 - - + -
124H LEU 3.5 22.0 - - - +
125H ASP* 4.4 2.2 - - - +
133H PHE 3.4 14.5 + - - +
134H GLY 3.4 2.6 + - - -
135H ALA* 1.3 77.9 - - - +
137H LEU* 1.3 78.8 + - + +
139H LEU* 3.1 49.1 + - + +
140H VAL* 4.3 2.1 + - - +
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Residues in contact with LEU 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F LEU* 3.1 54.2 - - + +
138F ASN* 5.4 0.2 - - - +
140F VAL* 3.8 26.9 - - + -
141F PRO* 3.9 10.8 - - + -
25H LEU* 4.4 8.5 - - + -
125H ASP* 4.3 16.6 - - + +
132H PRO* 3.7 35.4 - - + +
133H PHE 5.3 0.2 - - - +
134H GLY 5.1 0.6 + - - -
135H ALA 3.2 1.6 + - - -
136H ILE* 1.3 82.7 - - + +
138H ASN* 1.3 58.0 + - - +
139H LEU 3.0 5.8 - - - -
140H VAL* 3.1 25.8 + - + +
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Residues in contact with ASN 138 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ARG 5.4 0.2 - - - +
132F PRO* 3.5 26.7 - - + +
137F LEU* 5.3 0.3 - - - +
106H VAL* 3.8 17.3 - - + +
135H ALA* 3.0 29.1 + - - +
137H LEU* 1.3 77.7 - - - +
139H LEU* 1.3 59.2 + - - +
140H VAL 3.3 0.4 - - - -
141H PRO* 3.4 13.3 - - - +
142H LEU* 3.2 20.3 - - - +
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Residues in contact with LEU 139 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H ILE* 4.3 14.8 - - + -
23H VAL* 4.2 16.6 - - + -
105H ILE* 3.9 19.7 - - + -
106H VAL* 4.2 20.4 - - + +
109H CYS* 3.8 26.0 - - + -
121H VAL* 4.0 20.2 - - + -
135H ALA 4.2 0.4 + - - -
136H ILE* 3.1 37.3 + - + +
137H LEU 3.0 0.4 - - - -
138H ASN* 1.3 79.7 - - - +
140H VAL* 1.3 56.6 + - - +
141H PRO 3.4 0.2 - - - -
142H LEU* 2.9 27.2 + - + +
143H ALA* 3.0 15.1 + - - +
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Residues in contact with VAL 140 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25F LEU* 3.9 27.4 - - + -
125F ASP* 3.9 14.1 - - + +
137F LEU* 4.1 10.3 - - + -
140F VAL* 5.5 2.7 - - + -
148F LYS* 3.2 15.7 + - + -
23H VAL* 5.3 4.3 - - + -
25H LEU* 4.7 7.4 - - + -
136H ILE 4.8 2.0 - - - +
137H LEU* 3.4 35.7 - - + +
139H LEU* 1.3 76.6 - - + +
141H PRO* 1.3 64.7 - - + +
142H LEU 3.1 1.0 + - - -
143H ALA* 3.2 12.1 + - - +
146H VAL* 4.2 31.7 - - + +
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Residues in contact with PRO 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ASP* 3.5 24.4 - - - +
126F GLY* 3.9 14.3 - - - -
130F ARG* 3.5 32.9 - - - +
132F PRO* 3.7 24.7 - - + -
137F LEU* 3.8 7.9 - - + -
148F LYS* 4.5 1.7 + - - -
162F TYR* 3.5 21.9 - - - -
137H LEU 3.5 7.0 - - - +
138H ASN 3.4 15.3 - - - +
140H VAL* 1.3 93.6 - - + +
142H LEU* 1.3 56.1 + - - +
143H ALA 3.5 0.2 - - - -
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Residues in contact with LEU 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F ARG* 3.6 52.7 + - + +
162F TYR* 2.8 9.4 + - - -
186F ARG* 2.8 29.1 + - - -
21H ILE* 4.0 8.4 - - + +
106H VAL* 3.7 25.6 - - + -
110H GLU* 3.8 23.6 - - + +
138H ASN 3.2 22.7 - - - +
139H LEU* 2.9 14.8 + - + +
141H PRO* 1.3 78.1 - - - +
143H ALA* 1.3 57.9 + - - +
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Residues in contact with ALA 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F LYS* 2.8 28.9 + - - -
161F ALA* 3.8 3.3 - - - +
162F TYR* 4.0 2.4 - - - -
21H ILE* 3.5 18.6 - - + +
23H VAL* 3.7 23.6 - - + -
139H LEU 3.0 12.1 + - - +
140H VAL 3.2 7.5 + - - +
141H PRO 3.5 0.2 - - - -
142H LEU* 1.3 79.8 - - - +
144H GLU* 1.3 62.8 + - - +
145H SER 3.8 1.3 - - - +
146H VAL* 3.8 12.3 - - + -
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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