Contacts of the strand formed by residues 41 - 52 (chain B) in PDB entry 5ITX
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 GLU 41 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLY* 3.2 19.2 - - - +
26B CYS* 3.6 23.4 - - - -
40B PHE* 1.3 76.1 - - - +
42B SER* 1.3 64.1 + - - +
68B PRO* 4.0 27.5 - - + +
70B GLN* 3.3 24.9 + - - +
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Residues in contact with SER 42 (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 GLY* 2.9 8.0 - - - -
25B GLY* 2.6 38.3 + - - -
40B PHE* 4.1 13.2 - - - -
41B GLU* 1.3 78.3 + - - +
43B SER* 1.3 59.0 + - - +
44B ALA 3.4 15.7 + - - -
45B TYR* 3.8 20.6 - - - -
62B PRO* 3.5 16.6 - - - +
66B ALA* 3.7 7.4 - - - +
67B GLN 3.7 8.1 + - - -
68B PRO* 4.6 2.1 + - - -
70B GLN* 4.9 0.4 - - - +
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Residues in contact with SER 43 (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 GLY* 3.9 9.4 - - - -
25B GLY 4.8 0.7 - - - +
42B SER* 1.3 73.1 + - - +
44B ALA* 1.3 63.5 + - - +
66B ALA* 3.6 6.8 - - - -
67B GLN* 2.9 36.8 + - - +
104B ALA* 3.9 12.1 - - - +
105B PRO* 5.5 1.0 - - - +
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Residues in contact with ALA 44 (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 VAL* 3.6 18.6 - - + -
23B PHE 3.1 7.9 - - - -
42B SER* 3.1 7.3 + - - -
43B SER* 1.3 84.1 + - - +
45B TYR* 1.3 60.3 + - - +
62B PRO* 3.3 5.4 - - - +
63B LEU* 2.9 37.5 + - + -
66B ALA* 3.5 7.4 - - + +
261E ARG* 4.2 10.8 - - - +
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Residues in contact with TYR 45 (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 VAL* 3.6 4.0 - - - +
23B PHE* 2.7 65.5 + - + +
24B GLY* 3.3 27.3 + - - -
25B GLY 4.2 4.5 - - - -
26B CYS 4.7 3.3 + - - -
27B VAL* 3.9 8.0 - - + +
40B PHE* 3.6 37.2 - + + -
42B SER* 3.8 10.8 - - - -
44B ALA* 1.3 75.4 - - - +
46B ARG* 1.3 66.4 + - - +
47B ILE* 3.9 7.0 - - + -
60B LEU* 3.8 29.8 - - + -
61B SER 3.2 21.1 - - - +
62B PRO* 3.7 4.3 - - + -
63B LEU* 4.1 3.6 - - - +
101B PHE* 3.7 25.2 - + - +
102B TYR 4.2 2.4 + - - -
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Residues in contact with ARG 46 (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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18B CYS 6.0 1.6 - - - +
19B ARG 4.6 12.1 + - - -
20B ALA 5.4 2.2 - - - -
21B LEU 3.9 14.7 + - - +
22B VAL* 3.5 23.6 - - + +
23B PHE* 4.9 0.7 - - - -
45B TYR* 1.3 74.0 - - - +
47B ILE* 1.3 64.7 + - - +
59B ILE 3.4 2.4 - - - +
60B LEU* 3.4 3.1 - - - -
61B SER* 2.9 39.8 + - - +
63B LEU* 3.6 37.5 - - + +
258E ALA 3.8 15.8 + - - -
260E LEU 3.8 12.5 + - - -
261E ARG* 4.6 8.1 - - - +
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Residues in contact with ILE 47 (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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14B VAL* 4.2 6.1 - - + +
15B ASN* 4.7 1.2 - - - +
18B CYS* 3.8 24.4 + - + +
23B PHE* 3.5 42.5 - - + -
45B TYR* 3.9 4.0 - - + -
46B ARG* 1.3 79.0 - - - +
48B SER* 1.3 61.8 + - - +
58B LEU* 3.9 26.7 - - + -
59B ILE 3.3 7.6 - - - +
60B LEU* 3.9 16.2 - - + -
101B PHE* 3.7 35.9 - - + -
112B LEU* 3.7 15.3 - - + -
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Residues in contact with SER 48 (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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14B VAL* 4.7 1.6 - - - -
15B ASN* 3.3 14.6 - - - -
46B ARG 4.2 0.2 - - - -
47B ILE* 1.3 77.4 - - - +
49B ALA* 1.3 64.4 + - - +
58B LEU* 3.3 6.4 - - - +
59B ILE* 2.8 48.4 + - - +
61B SER* 5.4 1.7 + - - -
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Residues in contact with ALA 49 (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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11B SER* 3.1 29.2 - - - +
14B VAL* 3.8 21.3 - - + -
15B ASN* 2.6 29.5 + - - +
48B SER* 1.3 76.3 - - - +
50B SER* 1.3 63.7 + - - +
56B LEU* 4.6 4.9 - - + -
57B ARG 3.4 7.0 - - - +
58B LEU* 4.0 8.7 - - + -
59B ILE* 6.4 0.2 - - - -
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Residues in contact with SER 50 (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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11B SER* 2.9 12.0 + - - -
49B ALA* 1.3 75.6 - - - +
51B ALA* 1.3 59.3 + - - +
56B LEU* 3.5 3.6 - - - +
57B ARG* 2.8 43.2 + - - +
129B TRP* 4.0 16.3 - - - -
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Residues in contact with ALA 51 (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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7B LEU* 3.8 26.9 - - + +
8B HIS* 4.0 21.3 - - + +
11B SER* 3.6 5.9 + - - -
50B SER* 1.3 76.1 + - - +
52B ARG* 1.3 64.5 + - - +
53B GLY 4.3 1.1 - - - +
55B GLU 3.5 10.5 - - - +
56B LEU* 4.3 2.0 - - - +
129B TRP* 4.2 3.8 - - - -
136B CYS* 5.1 0.6 - - - -
139B GLN* 3.4 20.6 + - - +
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Residues in contact with ARG 52 (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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51B ALA* 1.3 78.5 - - - +
53B GLY* 1.3 66.7 + - - +
54B LYS 3.2 0.5 + - - -
55B GLU* 2.9 29.7 + - - +
129B TRP* 3.6 61.6 - - + +
130B GLN 4.8 0.8 + - - -
133B ARG* 3.5 21.8 + - - +
134B GLY 3.1 24.2 + - - -
135B PRO* 3.9 5.9 - - - +
136B CYS* 3.8 11.4 - - + -
139B GLN* 6.4 0.2 - - + -
140B GLU* 3.1 26.8 + - - +
172B ASN* 3.5 22.6 + - - +
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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