Contacts of the strand formed by residues 38 - 44 (chain A) in PDB entry 4XCS
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 TYR 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LYS* 1.3 76.1 - - - +
39A VAL* 1.3 61.8 + - - +
70A ASN* 3.0 9.5 + - - +
71A CYS* 3.2 22.1 - - + -
72A GLN 2.8 24.3 + - - -
132A ILE* 3.9 20.4 - - + -
133A ILE 3.4 14.1 - - - -
134A ASP* 3.3 13.6 - - + +
135A ASP* 3.6 23.1 - - + +
140A ARG* 3.3 15.6 + - + -
160A VAL* 4.3 11.2 - - + -
163A PHE* 3.3 33.1 - + + +
164A GLN* 3.5 31.4 - - + +
167A ASP* 2.6 28.8 + - - -
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LEU* 4.2 17.0 - - + -
34A TYR* 3.7 31.6 - - + -
37A LYS 4.0 4.9 - - - +
38A TYR* 1.3 81.3 - - - +
40A VAL* 1.3 75.1 + - - +
41A PHE* 4.2 11.7 - - + +
71A CYS* 4.3 0.2 - - - -
72A GLN* 3.3 13.0 - - + +
74A ILE* 3.8 21.1 - - + -
131A PHE 3.7 0.9 - - - +
132A ILE* 3.6 6.2 - - - +
133A ILE* 2.9 47.4 + - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 1.3 73.4 - - - +
41A PHE* 1.3 54.0 + - - +
42A PHE* 3.7 18.2 - - + -
59A PHE* 5.1 0.4 - - + -
66A PHE* 4.2 9.4 - - + -
71A CYS* 3.5 23.5 - - - -
72A GLN 3.0 6.3 + - - +
73A VAL* 3.4 13.4 - - + +
74A ILE 2.8 33.1 + - - +
130A LEU* 3.6 26.2 - - + -
131A PHE 3.7 2.7 - - - -
132A ILE* 3.9 8.5 - - + -
156A THR* 4.1 11.0 - - + -
160A VAL* 3.7 20.9 - - + -
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE* 3.8 30.5 - + - -
31A LEU* 5.7 0.9 - - + -
39A VAL* 3.9 5.1 - - + -
40A VAL* 1.3 72.0 - - - +
42A PHE* 1.3 61.1 + - - +
43A PHE* 4.1 9.0 - + + -
74A ILE* 3.5 26.0 - - + -
76A ALA* 3.6 30.7 - - + -
105A VAL* 5.1 0.7 - - + -
112A ILE* 4.0 18.8 - - + -
116A TYR* 4.1 32.3 - + - -
130A LEU* 3.5 3.6 - - - +
131A PHE* 2.8 63.6 + + + +
133A ILE* 3.9 16.6 - - + -
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A VAL* 3.7 17.7 - - + -
41A PHE* 1.3 73.5 - - - +
43A PHE* 1.3 56.9 + - - +
44A TYR* 4.0 32.3 - + + -
55A GLU* 5.0 4.3 - - + -
59A PHE* 3.5 56.3 - + + -
73A VAL* 4.2 9.9 - - + -
74A ILE 3.0 16.8 + - - +
75A GLY* 3.6 5.2 - - - -
76A ALA* 2.8 35.0 + - - +
102A ILE* 5.9 1.1 - - + -
128A ARG* 6.5 0.9 - - + -
129A GLY 3.6 4.9 - - - +
130A LEU* 4.0 12.3 - - + -
151A ARG* 3.6 26.5 - - + -
201A GOL 4.1 8.7 - - - -
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.9 9.1 + + + -
42A PHE* 1.3 72.9 - - - +
44A TYR* 1.3 80.0 + - - +
45A PRO* 3.4 14.0 - - + +
76A ALA* 3.5 23.6 - - + -
77A SER 4.4 3.4 - - - -
78A VAL* 4.2 7.2 - - + -
107A ASP* 3.3 33.9 - - + -
112A ILE* 3.6 30.7 - - + -
113A ALA* 3.6 21.1 - - + -
116A TYR* 5.6 1.3 - - + -
118A VAL* 3.6 19.9 - - + +
128A ARG* 3.5 2.8 - - - +
129A GLY 2.9 37.8 + - - +
131A PHE* 4.1 20.6 - - + -
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Residues in contact with TYR 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 4.0 30.3 - + + -
43A PHE* 1.3 73.5 - - - +
45A PRO* 1.3 67.7 - - + +
46A LEU 3.2 17.8 + - - +
48A PHE* 3.7 11.7 - + - -
51A VAL* 3.4 29.8 - - + -
55A GLU* 2.6 34.5 + - - +
56A ILE* 3.3 35.1 - - + +
75A GLY* 5.5 2.5 - - - -
76A ALA 2.8 23.3 + - - +
77A SER* 3.2 24.4 - - - -
78A VAL 3.3 5.9 + - - -
128A ARG* 3.6 26.5 - - + -
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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