Contacts of the strand formed by residues 46 - 63 (chain A) in PDB entry 4R7X
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 SER 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A VAL* 3.5 12.3 - - - +
45A LYS* 1.3 86.7 - - - +
47A LEU* 1.3 60.3 + - - +
48A LYS* 3.6 23.9 + - - -
89A ILE 3.2 15.0 - - - -
91A HIS* 4.8 9.0 - - - -
141A GLU 3.8 0.4 - - - +
142A LEU* 3.9 0.5 - - - -
143A HIS* 2.9 53.3 + - - +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.4 4.3 - - + -
34A VAL* 4.4 22.4 - - + -
36A LEU* 5.3 7.2 - - + -
44A VAL* 4.8 3.1 - - + -
46A SER* 1.3 75.2 - - - +
48A LYS* 1.3 58.1 + - - +
49A ILE* 6.3 0.2 - - + -
87A ILE* 4.0 0.2 - - - +
88A LEU* 2.7 44.5 + - + +
89A ILE* 3.1 34.3 + - + +
112A TYR* 3.7 39.0 - - + -
140A ALA* 5.0 1.6 - - + -
141A GLU 3.4 25.8 - - - +
142A LEU* 4.2 15.0 - - + +
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 3.6 28.2 + - - +
47A LEU* 1.3 79.8 - - - +
49A ILE* 1.3 67.1 + - - +
86A ASP 3.5 8.7 - - - +
87A ILE* 4.2 31.9 - - + -
91A HIS* 4.9 5.0 - - - +
140A ALA* 3.6 2.8 - - - +
141A GLU* 2.8 49.3 + - - +
143A HIS* 4.6 15.3 + - + +
205B PO4 5.0 5.9 + - - +
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Residues in contact with ILE 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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34A VAL* 4.1 16.2 - - + -
47A LEU* 6.1 0.2 - - + -
48A LYS* 1.3 81.2 - - - +
50A HIS* 1.3 62.6 + - - +
51A ALA* 5.9 1.6 - - + +
84A HIS* 5.3 4.3 - - + +
85A LYS* 3.5 4.9 - - - +
86A ASP* 2.9 60.2 + - + +
88A LEU* 3.7 26.5 - - + -
114A PHE* 3.7 33.9 - - + -
115A SER 5.1 2.5 - - - +
116A PHE* 4.5 17.3 - - + -
138A VAL* 4.6 9.4 - - + -
139A LYS 3.2 9.0 - - - +
140A ALA* 4.7 2.5 - - - -
141A GLU* 5.3 0.4 - - - -
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Residues in contact with HIS 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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49A ILE* 1.3 75.1 - - - +
51A ALA* 1.3 72.3 + - - +
52A ARG* 3.2 28.8 + - + -
83A ASN* 2.9 26.4 + - - -
84A HIS 3.5 8.3 - - - -
85A LYS* 3.7 16.0 - - + -
137A TRP* 3.4 12.9 - + - -
138A VAL* 4.5 1.6 - - - -
139A LYS* 2.8 39.2 + - + -
141A GLU* 3.7 17.3 - - - +
202A PO4 3.5 16.2 + - - -
203A PO4 2.8 29.7 + - - -
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ILE* 4.2 2.1 - - + +
50A HIS* 1.3 76.1 - - - +
52A ARG* 1.3 65.3 + - - +
82A PHE* 3.7 15.9 - - + -
83A ASN* 3.4 1.4 - - - -
84A HIS* 2.7 42.1 + - + +
116A PHE* 3.6 37.7 - - + -
137A TRP 3.4 9.0 - - - +
138A VAL* 4.4 3.8 - - + +
156A PHE* 5.3 0.4 - - + -
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Residues in contact with ARG 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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50A HIS* 3.2 23.9 + - - +
51A ALA* 1.3 77.3 - - - +
53A GLY* 1.3 65.0 + - - +
54A HIS* 3.7 24.7 - - - +
78A GLU* 4.4 5.6 + - - -
80A GLU* 3.2 24.0 + - - -
82A PHE* 3.3 18.8 - - - +
83A ASN* 3.1 15.3 + - - +
135A ARG 4.0 0.3 - - - +
136A TYR* 3.3 2.8 - - - +
137A TRP* 2.9 59.5 + - + +
156A PHE* 5.0 0.9 - - - -
203A PO4 4.5 0.7 - - - -
205A PO4 3.6 6.3 + - - -
139B LYS* 4.3 5.3 - - - +
151B LYS* 3.4 6.1 - - - +
201B PO4 2.8 39.8 + - - -
203B PO4 3.7 16.4 + - - -
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Residues in contact with GLY 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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52A ARG* 1.3 75.5 - - - +
54A HIS* 1.3 63.4 + - - +
80A GLU* 3.7 0.9 - - - -
81A TYR* 2.8 28.3 + - - -
82A PHE* 3.0 17.0 + - - +
135A ARG 3.2 11.0 - - - -
136A TYR* 3.5 23.4 - - - -
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Residues in contact with HIS 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 3.7 18.6 - - - +
53A GLY* 1.3 74.4 - - - +
55A ALA* 1.3 71.7 + - - +
56A LYS* 3.6 19.6 - - + +
78A GLU* 4.0 21.4 - - + -
79A VAL 3.2 21.5 - - - +
80A GLU* 3.8 9.2 - - + -
81A TYR* 3.8 9.1 - - - -
133A SER 3.9 0.3 - - - +
134A VAL* 3.3 4.8 - - - +
135A ARG* 3.0 34.0 + - - +
137A TRP* 3.5 25.3 + + - -
201A PO4 3.1 32.3 + - - -
203B PO4 5.6 0.7 - - - -
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Residues in contact with ALA 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 HIS* 1.3 75.4 - - - +
56A LYS* 1.3 60.2 + - - +
77A GLU 3.7 0.6 - - - +
78A GLU* 3.1 6.6 - - - -
79A VAL* 3.0 39.5 + - + +
81A TYR* 3.6 24.7 - - + +
133A SER 3.2 8.7 - - - +
134A VAL* 4.0 10.8 - - + -
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Residues in contact with LYS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A HIS* 3.6 15.5 - - + +
55A ALA* 1.3 76.0 - - - +
57A VAL* 1.3 65.1 + - - +
58A ARG* 3.0 39.9 - - + +
76A THR* 3.3 32.0 + - + +
77A GLU 3.4 4.9 - - - +
78A GLU* 4.2 8.7 - - + -
131A HIS 3.8 0.3 - - - +
132A GLY* 3.3 3.3 - - - -
133A SER* 2.7 44.9 + - - +
135A ARG* 4.3 9.2 - - - +
201A PO4 3.3 42.8 - - - +
153B LYS* 5.0 6.2 - - - +
202B PO4 5.4 2.1 + - - -
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Residues in contact with VAL 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 LYS* 1.3 77.4 - - - +
58A ARG* 1.3 69.1 + - - +
59A TRP* 3.5 18.0 - - + -
76A THR* 3.4 5.1 - - - -
77A GLU* 3.0 60.2 + - + +
131A HIS* 3.1 20.0 - - + +
132A GLY* 4.6 2.9 - - - -
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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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56A LYS* 3.0 32.2 - - + +
57A VAL* 1.3 73.5 - - - +
59A TRP* 1.3 64.2 + - - +
60A THR* 6.5 0.4 - - + -
75A TYR 3.7 4.5 - - - +
76A THR* 4.0 9.8 + - - +
131A HIS* 3.2 30.9 + - - +
135A ARG* 3.1 36.0 - - - +
201A PO4 3.5 12.7 + - - -
56B LYS* 4.4 1.4 - - - +
58B ARG* 2.9 37.6 - - - +
135B ARG* 5.4 1.2 - - - +
202B PO4 4.0 11.5 + - - -
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Residues in contact with TRP 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 VAL* 3.5 26.9 - - + -
58A ARG* 1.3 76.3 - - - +
60A THR* 1.3 74.2 + - - +
61A GLU* 3.7 24.1 + - + -
75A TYR* 3.0 70.0 + + + +
77A GLU* 3.7 31.4 - - + -
131A HIS* 5.9 0.7 - - + -
152B LEU* 3.8 24.0 - - + -
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Residues in contact with THR 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 ARG* 6.5 0.2 - - + -
59A TRP* 1.3 83.5 - - - +
61A GLU* 1.3 71.2 + - - +
62A SER* 5.8 0.3 + - - -
72A THR* 3.7 20.0 - - + +
73A GLN 3.4 5.4 - - - -
74A ASN* 3.2 23.6 - - + +
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Residues in contact with GLU 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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59A TRP* 3.7 22.9 + - + -
60A THR* 1.3 80.1 - - - +
62A SER* 1.3 64.1 + - - +
63A ARG* 3.8 24.5 + - - +
72A THR* 4.6 2.5 - - - -
73A GLN* 3.0 34.9 + - - +
75A TYR* 4.3 14.3 - - + -
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Residues in contact with SER 62 (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 THR* 5.8 0.5 + - - -
61A GLU* 1.3 73.4 - - - +
63A ARG* 1.3 69.2 + - - +
71A TYR 3.9 8.5 - - - -
72A THR* 4.4 10.8 + - - +
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Residues in contact with ARG 63 (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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61A GLU* 4.0 29.4 + - - +
62A SER* 1.3 84.6 - - - +
64A ASN* 1.3 78.8 + - - +
70A ALA* 3.2 15.6 - - - +
71A TYR* 3.1 52.6 + - + +
73A GLN* 4.5 8.0 - - + +
75A TYR* 3.1 26.3 + - - -
154B LYS* 5.0 3.2 - - - +
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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