Contacts of the strand formed by residues 20 - 26 (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 GLN 20 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H ARG 4.8 2.7 - - - +
19H GLY* 1.3 76.5 - - - +
21H ILE* 1.3 65.1 + - - +
22H GLN* 2.9 41.1 + - - +
43H PHE* 5.2 3.6 - - - -
113H ALA* 3.7 5.9 - - - +
117H LYS 3.1 7.5 + - - +
118H THR* 3.8 23.7 + - + +
119H VAL* 2.8 27.3 + - - +
144H GLU* 3.4 29.7 - - + +
145H SER* 4.9 4.8 - - - -
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Residues in contact with ILE 21 (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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186F ARG* 3.4 18.8 - - - +
20H GLN* 1.3 79.2 - - - +
22H GLN* 1.3 65.2 + - - +
23H VAL* 4.0 21.3 - - + -
109H CYS* 3.7 35.9 - - + +
110H GLU* 3.9 10.5 - - - +
113H ALA* 3.7 9.6 - - + -
119H VAL* 3.3 9.2 - - + +
121H VAL* 4.7 7.6 - - + -
139H LEU* 4.3 18.6 - - + -
142H LEU* 4.0 8.3 - - + +
143H ALA* 3.5 9.7 - - + +
144H GLU* 2.9 39.3 + - - +
145H SER 3.5 3.8 + - - -
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Residues in contact with GLN 22 (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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20H GLN* 2.9 42.1 + - + +
21H ILE* 1.3 74.6 - - - +
23H VAL* 1.3 64.7 + - - +
39H ARG* 2.7 42.1 + - - +
42H ARG* 5.8 2.4 - - - +
43H PHE* 5.1 7.1 - - - -
118H THR* 4.4 7.6 - - + +
119H VAL 2.8 13.1 + - - +
120H ILE* 3.5 16.9 - - + +
121H VAL* 2.8 28.6 + - - +
145H SER* 3.5 15.0 - - - -
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Residues in contact with VAL 23 (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* 4.0 10.8 - - + -
22H GLN* 1.3 79.7 - - - +
24H ILE* 1.3 65.9 + - - +
25H LEU* 3.8 32.1 - - + -
39H ARG* 4.8 2.3 + - - +
121H VAL* 3.5 7.0 - - + +
123H ALA* 5.6 0.4 - - + -
136H ILE* 4.7 13.5 - - + +
139H LEU* 4.2 21.3 - - + +
140H VAL* 5.2 4.3 - - + +
143H ALA* 3.7 23.6 - - + -
145H SER 2.8 12.3 + - - +
146H VAL* 3.5 11.5 - - + -
147H VAL* 3.0 26.7 + - - +
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Residues in contact with ILE 24 (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* 1.3 73.4 - - - +
25H LEU* 1.3 62.8 + - - +
32H LYS* 3.8 13.6 - - - +
35H GLU* 3.9 7.6 - - + -
36H LEU* 3.8 27.8 - - + +
39H ARG* 3.6 35.0 - - - +
120H ILE* 3.7 27.4 - - + -
121H VAL 2.7 14.5 + - - +
122H ALA* 3.4 3.6 - - + -
123H ALA 2.9 28.4 + - - +
147H VAL* 3.8 5.6 - - + -
149H LEU* 3.8 33.9 - - + -
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Residues in contact with LEU 25 (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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140F VAL* 3.9 27.4 - - + -
146F VAL* 5.8 1.3 - - + -
23H VAL* 3.8 22.9 - - + -
24H ILE* 1.3 75.9 - - - +
26H GLY* 1.3 54.2 + - - +
32H LYS* 3.8 5.4 - - - +
123H ALA* 3.3 22.7 - - + +
124H LEU 4.3 0.4 - - - -
125H ASP* 3.9 21.8 - - + +
136H ILE* 4.4 10.1 - - + +
137H LEU* 4.4 7.2 - - + -
140H VAL* 4.7 5.8 - - + -
146H VAL* 4.2 18.8 - - + -
147H VAL 2.8 14.4 + - - +
148H LYS* 3.9 9.6 - - + -
149H LEU* 2.7 36.4 + - - +
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Residues in contact with GLY 26 (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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25H LEU* 1.3 78.2 - - - +
27H PRO* 1.3 78.2 - - - +
30H SER* 4.0 5.8 - - - -
32H LYS* 3.7 2.5 - - - +
123H ALA 3.6 2.0 + - - -
124H LEU* 3.3 19.1 - - - +
125H ASP* 3.2 19.6 + - - +
148H LYS* 4.0 4.7 - - - -
149H LEU 3.6 8.5 - - - -
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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