Contacts of the strand formed by residues 22 - 32 (chain B) in PDB entry 5IXC
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 TRP 22 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B SER* 5.3 1.1 - - - -
20B THR* 3.6 32.3 - - - -
21B CYS* 1.3 74.8 - - - +
23B GLN* 1.3 59.2 + - - +
79B LEU* 3.4 9.2 - - - +
80B ILE* 2.8 34.9 + - - +
82B SER* 3.3 33.9 - - - -
116B PRO* 3.6 28.1 - - + +
140B MET* 3.4 33.4 - - + -
141B GLU 3.2 29.4 - - - -
142B GLU* 3.5 33.7 - - + +
143B THR* 4.6 0.7 - - - -
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Residues in contact with GLN 23 (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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22B TRP* 1.3 71.0 - - - +
24B LEU* 1.3 61.7 + - - +
25B THR* 3.4 10.6 - - - +
77B ARG* 3.8 34.2 + - + +
78B PHE 3.5 14.4 - - - +
79B LEU* 4.2 11.4 - - + +
139B LEU 3.3 4.5 - - - +
140B MET* 3.4 2.3 - - - -
141B GLU* 2.8 68.9 + - + +
142B GLU 5.3 0.4 - - - +
143B THR* 4.9 9.2 - - - -
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Residues in contact with LEU 24 (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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22B TRP 3.8 1.6 + - - -
23B GLN* 1.3 73.0 - - - +
25B THR* 1.3 64.2 + - - +
26B VAL* 3.7 22.2 - - + -
51B LEU* 5.7 1.8 - - + -
76B PHE 3.7 0.5 - - - +
77B ARG* 3.4 2.8 - - - +
78B PHE* 2.9 40.4 + - + +
80B ILE* 3.7 22.9 - - + -
88B LEU* 5.1 2.5 - - + -
111B ILE* 3.8 33.2 - - + -
114B VAL* 4.0 14.4 - - + -
138B PHE* 4.2 14.8 - - + -
139B LEU 3.4 10.3 - - - +
140B MET* 3.7 25.6 - - + -
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Residues in contact with THR 25 (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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23B GLN* 3.4 24.7 - - - +
24B LEU* 1.3 76.3 - - - +
26B VAL* 1.3 62.4 + - - +
27B ARG* 4.2 8.7 + - - -
75B ALA* 5.5 5.7 - - - +
76B PHE 3.1 11.4 - - - -
77B ARG* 3.8 18.6 - - + +
137B GLU 3.7 0.9 - - - +
138B PHE* 3.5 3.1 - - - -
139B LEU* 2.9 48.2 + - + +
141B GLU* 4.0 10.1 - - - +
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Residues in contact with VAL 26 (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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24B LEU* 3.7 28.0 - - + -
25B THR* 1.3 77.0 - - - +
27B ARG* 1.3 59.4 + - - +
28B VAL* 4.6 4.9 - - + -
49B LEU* 3.3 38.1 - - + -
74B GLU 4.0 0.7 - - - +
75B ALA* 3.5 1.1 - - - -
76B PHE* 2.8 30.0 + - - +
78B PHE* 3.7 17.9 - - + -
88B LEU* 4.2 7.2 - - + -
136B VAL* 4.5 5.8 - - + -
137B GLU 3.3 4.9 - - - +
138B PHE* 3.7 23.1 - - + -
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Residues in contact with ARG 27 (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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25B THR* 4.1 9.2 + - - +
26B VAL* 1.3 73.9 - - - +
28B VAL* 1.3 60.8 + - - +
29B LEU* 3.5 23.9 + - + +
73B ASN* 3.8 20.2 + - - +
74B GLU 3.0 13.4 + - - +
75B ALA* 3.7 23.4 - - + +
119B LEU* 5.6 3.4 - - - +
136B VAL* 3.4 7.1 - - - +
137B GLU* 2.9 71.5 + - + +
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Residues in contact with VAL 28 (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 VAL* 4.6 3.4 - - + -
27B ARG* 1.3 70.9 - - - +
29B LEU* 1.3 58.9 + - - +
47B VAL* 3.7 36.8 - - + -
49B LEU* 4.2 27.6 - - + -
61B THR* 4.2 9.6 - - + -
72B TRP* 3.8 14.8 - - + +
73B ASN* 3.0 6.2 + - - -
74B GLU 2.7 34.4 + - - +
76B PHE* 4.3 15.9 - - + -
134B LEU* 4.4 11.2 - - + -
135B ASP 4.2 3.1 - - - +
136B VAL* 4.6 9.4 - - + -
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Residues in contact with LEU 29 (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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27B ARG* 3.6 24.7 - - + +
28B VAL* 1.3 71.4 - - - +
30B GLU* 1.3 66.2 + - + +
71B VAL* 3.6 4.3 - - - +
72B TRP* 2.8 33.7 + - - +
73B ASN* 3.1 34.4 + - + +
121B ARG* 4.7 15.0 - - - +
135B ASP* 3.0 36.5 + - + +
136B VAL 4.4 1.3 - - - -
137B GLU* 4.1 29.2 - - + +
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Residues in contact with GLU 30 (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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28B VAL* 5.2 0.2 - - - +
29B LEU* 1.3 88.8 - - + +
31B ALA* 1.3 63.9 + - - +
32B ARG* 3.0 26.1 + - - +
69B HIS* 3.2 24.2 + - + -
70B PRO 3.1 15.3 - - - +
71B VAL* 4.1 15.9 - - + +
72B TRP* 4.2 3.4 - - - -
134B LEU* 3.4 9.1 - - - +
135B ASP* 2.8 34.5 + - - +
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Residues in contact with ALA 31 (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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30B GLU* 1.3 74.9 - - - +
32B ARG* 1.3 70.2 + - - +
34B LEU* 3.8 22.0 - - + -
69B HIS* 3.3 25.6 + - - -
70B PRO* 3.1 18.2 + - + +
72B TRP* 3.9 14.9 - - + -
92B ILE* 4.0 11.2 - - + -
133B GLU 3.0 12.8 - - - +
134B LEU* 4.0 1.6 - - + -
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Residues in contact with ARG 32 (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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30B GLU* 3.0 21.4 + - - +
31B ALA* 1.3 79.3 - - - +
33B ASN* 1.3 83.7 + - - +
34B LEU* 3.3 5.6 + - - +
68B SER 3.6 2.9 - - - -
69B HIS* 3.4 30.5 - - + +
123B THR* 3.8 5.1 + - - +
132B GLU* 3.4 2.3 - - - +
133B GLU* 2.7 68.3 + - + +
135B ASP* 2.9 42.2 + - - -
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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