Contacts of the strand formed by residues 48 - 59 (chain A) in PDB entry 1XEH
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 LYS 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 5.5 0.9 - - - -
46A CYS 3.9 12.1 - - - +
47A ARG* 1.3 76.0 - - - +
49A LEU* 1.3 61.6 + - - +
50A PHE* 3.8 30.7 + - + -
81A GLN* 3.4 28.4 + - - +
83A VAL* 3.4 15.7 - - - +
84A PRO* 4.3 9.9 - - + -
146A PHE 3.9 0.7 - - - +
147A CYS* 3.6 3.3 - - - -
148A ALA 3.0 29.2 + - - +
149A GLU* 4.1 16.8 + - - +
150A ASN* 4.4 8.7 + - - -
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Residues in contact with LEU 49 (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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14A LEU* 4.0 15.5 - - + -
37A VAL* 3.1 37.9 - - + -
39A VAL* 3.2 27.4 - - + -
44A LEU* 5.5 3.4 - - + -
48A LYS* 1.3 71.2 - - - +
50A PHE* 1.3 67.7 + - - +
51A VAL* 5.0 0.2 - - + -
81A GLN* 4.3 0.2 - - - -
82A VAL* 3.1 39.2 + - + +
83A VAL* 3.1 19.5 + - + +
110A TYR* 6.1 0.2 - - + -
145A SER* 4.3 1.6 - - - -
146A PHE 3.2 36.6 - - - +
147A CYS* 3.9 9.4 - - - +
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Residues in contact with PHE 50 (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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48A LYS* 3.8 27.8 - - + -
49A LEU* 1.3 74.0 - - - +
51A VAL* 1.3 65.6 + - - +
79A THR* 4.1 13.5 - - + -
80A LEU 3.7 15.7 - - - +
81A GLN* 4.1 30.7 - - + -
144A LYS 3.9 0.2 - - - +
145A SER* 3.3 4.7 - - - -
146A PHE* 3.0 68.4 + + + -
148A ALA* 3.5 28.3 - - + -
150A ASN* 4.2 5.8 - - - -
151A PRO* 3.9 31.9 - - + -
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Residues in contact with VAL 51 (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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37A VAL* 4.0 8.3 - - + -
49A LEU* 5.0 0.7 - - + -
50A PHE* 1.3 79.6 - - - +
52A MET* 1.3 64.9 + - - +
78A GLN 4.1 0.7 - - - +
79A THR* 3.4 2.1 - - - +
80A LEU* 3.3 30.7 + - + +
82A VAL* 4.1 20.0 - - + -
112A PHE* 3.6 48.5 - - + -
114A LEU* 5.4 5.7 - - + +
143A VAL* 4.0 14.8 - - + -
144A LYS 3.6 4.3 - - - +
145A SER* 3.4 22.7 - - - +
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Residues in contact with MET 52 (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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51A VAL* 1.3 76.5 - - - +
53A LEU* 1.3 58.2 + - - +
54A THR* 4.1 14.4 - - + -
77A VAL* 3.9 23.8 - - + -
78A GLN 3.5 6.5 - - - +
79A THR* 3.3 32.1 - - + -
114A LEU* 5.1 0.9 - - - -
142A GLU 3.4 2.5 - - - +
143A VAL* 3.5 4.2 - - - +
144A LYS* 3.0 51.1 + - + +
146A PHE* 3.6 31.6 - - + -
151A PRO* 5.8 5.2 - - - -
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Residues in contact with LEU 53 (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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33A ILE* 3.6 14.4 - - + -
52A MET* 1.3 73.8 - - - +
54A THR* 1.3 70.5 + - - +
76A TYR* 3.9 14.7 - - + +
77A VAL* 3.7 3.1 - - - +
78A GLN* 3.3 25.7 + - + -
114A LEU* 3.0 51.1 - - + +
116A MET* 3.5 45.5 - - + -
141A PHE* 4.7 2.7 - - + -
142A GLU 3.4 15.5 - - - +
143A VAL* 4.0 11.2 - - + +
165A VAL* 5.3 0.2 - - + -
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Residues in contact with THR 54 (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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52A MET* 4.1 25.4 - - + -
53A LEU* 1.3 83.6 - - - +
55A CYS* 1.3 60.0 + - - +
56A ALA* 3.9 2.4 + - - -
58A ARG* 5.0 5.7 + - - -
74A ASP* 3.9 20.4 - - - +
76A TYR 3.6 4.0 - - - -
77A VAL* 4.3 9.2 - - + -
140A ASP 3.4 2.1 - - - +
141A PHE* 3.3 7.3 - - - +
142A GLU* 3.0 47.5 + - - +
144A LYS* 6.0 3.1 - - - +
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Residues in contact with CYS 55 (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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54A THR* 1.3 73.2 - - - +
56A ALA* 1.3 61.2 + - - +
74A ASP* 3.7 2.1 - - - -
75A LEU* 2.8 56.4 + - + +
76A TYR* 3.3 21.1 + - + +
120A LEU* 4.9 6.5 - - + -
121A PRO* 4.5 8.7 - - - -
139A ILE* 3.7 16.4 - - - -
140A ASP 3.4 4.9 - - - -
141A PHE* 3.4 31.9 - - + -
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Residues in contact with ALA 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A THR* 3.9 3.3 + - - -
55A CYS* 1.3 75.4 - - - +
57A PHE* 1.3 60.7 + - - +
58A ARG* 3.5 22.1 + - - +
72A ARG* 3.7 26.0 - - + -
73A LYS 3.3 11.9 - - - +
74A ASP* 4.1 9.2 - - - +
75A LEU* 4.5 5.6 - - - +
138A GLY 3.7 0.5 - - - +
139A ILE* 3.4 4.7 - - - +
140A ASP 3.1 31.3 + - - -
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Residues in contact with PHE 57 (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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56A ALA* 1.3 73.8 - - - +
58A ARG* 1.3 71.9 - - - +
59A TYR* 4.5 12.8 - + + -
71A PHE* 3.7 15.0 - + - +
72A ARG* 3.2 6.1 - - - -
73A LYS* 3.0 43.3 + - + +
75A LEU* 4.3 15.3 - - + +
137A CYS* 4.1 18.2 - - + -
138A GLY* 3.4 27.6 - - - -
139A ILE* 4.1 11.2 - - + -
238A VAL* 5.9 2.0 - - + -
240A LEU* 4.4 38.8 - - + -
241A TYR* 5.1 7.6 - + + -
313A GLY* 4.2 22.9 - - - -
314A ILE* 5.0 1.8 - - + -
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Residues in contact with ARG 58 (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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54A THR* 5.0 7.7 + - - -
56A ALA* 3.5 26.5 + - - +
57A PHE* 1.3 85.0 - - - +
59A TYR* 1.3 62.0 + - - +
62A ASP* 6.0 2.2 - - - +
65A GLU* 4.3 17.8 + - - +
70A THR* 6.5 0.7 - - - -
71A PHE 3.3 7.4 - - - +
72A ARG* 3.6 34.8 - - + +
137A CYS* 3.2 7.4 - - - +
138A GLY 2.9 31.7 + - - +
140A ASP* 3.3 51.4 + - - +
142A GLU* 3.9 22.2 + - - +
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Residues in contact with TYR 59 (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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57A PHE* 4.5 13.5 - + + -
58A ARG* 1.3 75.4 - - - +
60A GLY* 1.3 60.6 + - - +
69A LEU 4.6 0.7 - - - +
70A THR* 3.7 5.4 - - - -
71A PHE* 3.1 41.3 + - + +
134A GLY 3.5 11.7 - - - -
135A LYS* 3.2 52.9 - - + +
136A PRO 3.5 4.3 - - - -
137A CYS* 3.5 22.4 - - + -
238A VAL* 6.2 3.1 - - + -
241A TYR* 4.6 31.0 - + + -
242A SER* 5.7 7.4 - - - -
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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