Contacts of the strand formed by residues 52 - 61 (chain A) in PDB entry 4LAX
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 ARG 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A GLY 3.7 2.0 + - - -
51A ASP* 1.3 71.5 - - - +
53A VAL* 1.3 62.3 + - - +
54A PHE* 3.8 18.4 - - + -
78A SER* 3.5 24.2 - - - +
79A PHE* 3.4 10.4 - - - +
80A ASP* 2.9 35.9 + - - +
137A PHE* 3.1 5.9 - - - +
138A LYS* 2.9 51.0 + - + +
139A GLY 4.8 3.4 + - - +
140A GLU* 6.2 0.7 - - - -
146A GLU* 5.3 6.7 + - - -
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Residues in contact with VAL 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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47A PRO* 3.6 30.7 - - + -
51A ASP 4.2 8.7 - - - +
52A ARG* 1.3 76.3 - - - +
54A PHE* 1.3 64.2 + - - +
55A VAL* 3.6 17.0 - - + -
77A PHE 3.8 0.3 - - - +
78A SER* 3.2 9.7 + - - -
79A PHE* 2.9 46.8 + - + +
81A LEU* 4.4 7.6 - - + -
94A ILE* 3.7 18.6 - - + -
134A LEU* 3.6 19.3 - - + -
136A GLU 3.7 2.9 - - - -
137A PHE* 4.0 5.6 - - + -
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Residues in contact with PHE 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 ARG* 3.8 29.6 - - + -
53A VAL* 1.3 73.9 - - - +
55A VAL* 1.3 62.9 + - - +
76A LYS* 4.5 16.6 - - + -
77A PHE 3.5 4.9 - - - +
78A SER* 3.6 27.1 - - - -
134A LEU* 3.8 0.5 - - - +
135A PHE* 2.9 31.1 + - + +
136A GLU* 2.9 56.6 + - + +
138A LYS* 4.4 19.1 - - + -
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Residues in contact with VAL 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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53A VAL* 3.6 21.5 - - + -
54A PHE* 1.3 79.3 - - - +
56A HIS* 1.3 63.4 + - - +
76A LYS* 3.2 12.8 - - - +
77A PHE* 2.8 52.1 + - + +
79A PHE* 4.9 2.0 - - + -
90A TRP* 3.8 31.2 - - + -
94A ILE* 4.7 6.1 - - + -
132A VAL* 3.9 19.1 - - + -
133A GLU 3.1 14.8 - - - +
134A LEU* 4.0 9.0 - - + -
135A PHE* 4.1 1.3 - - - -
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Residues in contact with HIS 56 (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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55A VAL* 1.3 77.3 - - - +
57A TYR* 1.3 60.8 + - - +
70A SER* 2.8 39.6 + - - +
71A LEU* 4.0 34.8 - - + +
73A ARG 5.4 0.2 + - - -
74A LYS 4.4 5.6 + - - -
75A ASP* 3.6 17.5 + - - -
76A LYS* 3.7 29.0 - - + -
131A GLU 3.8 0.3 - - - +
132A VAL* 3.4 3.1 - - - +
133A GLU* 2.8 38.4 + - + +
135A PHE* 3.4 26.9 - + + -
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Residues in contact with TYR 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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55A VAL* 4.6 0.2 - - + -
56A HIS* 1.3 75.1 - - - +
58A THR* 1.3 72.4 + - - +
59A GLY 4.7 0.2 - - - -
68A ASP* 2.7 31.4 + - + -
69A SER* 3.2 6.7 + - - -
70A SER* 3.0 56.3 + - - -
71A LEU* 4.3 3.3 + - - +
77A PHE* 3.9 20.4 - + + -
90A TRP* 3.6 33.2 - + + -
130A PHE* 4.2 9.2 - + + -
131A GLU 3.0 11.2 - - - +
132A VAL* 4.3 2.2 - - + -
301A FK5 3.2 60.2 + - + +
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Residues in contact with THR 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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57A TYR* 1.3 75.9 + - - +
59A GLY* 1.3 62.0 + - - +
60A TRP* 3.6 40.7 - - + -
66A LYS* 4.0 16.2 - - + -
68A ASP 3.4 13.5 - - - +
69A SER* 3.0 20.7 + - - -
71A LEU* 4.3 8.8 - - - +
130A PHE* 3.3 5.7 - - - -
131A GLU* 2.9 39.1 + - - +
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Residues in contact with GLY 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 TYR* 4.2 1.8 - - - -
58A THR* 1.3 75.1 - - - +
60A TRP* 1.3 61.8 + - - -
66A LYS* 3.5 5.5 - - - +
67A PHE* 2.9 47.3 + - - -
68A ASP 2.8 17.4 + - - +
129A VAL 3.4 5.8 - - - -
130A PHE* 3.9 8.5 - - - -
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Residues in contact with TRP 60 (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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58A THR* 3.6 33.7 - - + -
59A GLY* 1.3 72.4 - - - -
61A LEU* 1.3 69.0 + - - +
64A GLY* 3.4 27.1 + - - -
65A THR 3.2 5.6 - - - +
66A LYS* 3.5 24.4 - - + +
67A PHE* 3.4 12.0 - - - -
104A HIS* 5.0 8.3 - + - -
128A LEU* 3.6 1.7 - - - -
129A VAL* 2.8 61.1 + - + +
130A PHE 4.6 0.4 - - - -
131A GLU* 3.7 37.9 - - + -
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Residues in contact with LEU 61 (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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60A TRP* 1.3 83.7 - - - +
62A LEU* 1.3 65.9 + - - +
63A ASP* 3.3 17.7 - - - +
64A GLY* 3.0 11.3 + - - -
65A THR* 2.8 33.9 + - + +
67A PHE* 3.7 13.6 - - + -
121A LYS 4.4 7.0 - - - +
122A ILE* 4.1 4.0 - - + -
123A PRO* 3.9 36.1 - - + -
126A ALA* 4.6 4.9 - - + -
127A THR 4.1 3.4 - - - +
128A LEU* 3.9 21.8 - - + -
129A VAL* 4.8 3.1 - - - +
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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