Contacts of the strand formed by residues 71 - 89 (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 TYR 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A SER* 3.9 3.3 - - - -
63A ARG* 3.1 55.8 + - + +
64A ASN* 4.2 10.8 - - - -
70A ALA* 1.3 79.9 - - - +
72A THR* 1.3 72.7 + - - +
73A GLN* 3.8 30.5 + - + +
20B ASN 4.1 7.3 + - - -
21B VAL* 3.7 38.1 - - + -
22B PRO* 3.4 27.1 - - + +
157B THR* 6.1 0.9 - - - -
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Residues in contact with THR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.7 31.0 - - + +
61A GLU 4.0 8.3 - - - +
62A SER* 4.4 9.8 + - - +
71A TYR* 1.3 86.0 + - - +
73A GLN* 1.3 63.1 + - - +
74A ASN* 3.8 16.2 + - - +
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Residues in contact with GLN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A THR* 3.4 3.8 - - - -
61A GLU 3.0 38.7 + - - +
63A ARG* 4.5 10.3 - - + +
71A TYR* 3.8 18.1 + - + +
72A THR* 1.3 71.4 - - - +
74A ASN* 1.3 83.0 + - - +
75A TYR* 3.5 34.6 - - + +
22B PRO* 3.6 22.3 - - - +
154B LYS* 3.4 17.3 - - - +
155B GLU* 2.5 35.8 + - - +
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Residues in contact with ASN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP 4.2 2.2 - - - -
60A THR* 3.2 25.4 - - + +
72A THR* 3.8 13.8 + - - +
73A GLN* 1.3 84.1 + - - +
75A TYR* 1.3 64.7 + - - +
76A THR* 6.1 0.2 - - - +
128B GLU* 4.4 11.9 + - - +
153B LYS 3.9 0.6 - - - +
154B LYS* 3.9 0.5 - - - -
155B GLU* 3.1 64.1 + - + +
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Residues in contact with TYR 75 (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* 3.7 3.3 - - - +
59A TRP* 3.0 77.1 + + + +
61A GLU* 4.3 19.3 - - + -
63A ARG* 3.1 24.4 + - - -
73A GLN* 3.5 29.5 - - + +
74A ASN* 1.3 79.4 - - - +
76A THR* 1.3 67.5 + - - +
10B THR* 6.3 1.8 - - - -
11B ILE 5.1 2.7 - - - -
152B LEU* 5.0 11.9 - - + -
153B LYS 3.4 4.9 - - - -
154B LYS* 3.4 46.2 + - + -
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Residues in contact with THR 76 (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* 3.3 43.2 + - + +
57A VAL 3.4 8.5 - - - +
58A ARG* 4.0 9.4 + - - +
59A TRP* 4.1 3.1 - - - -
75A TYR* 1.3 78.5 + - - +
77A GLU* 1.3 63.4 + - - +
78A GLU* 4.2 13.8 - - + +
151B LYS 3.9 0.2 - - - +
152B LEU* 3.4 4.2 - - - +
153B LYS* 2.6 59.8 + - + +
202B PO4 5.5 1.2 + - - -
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Residues in contact with GLU 77 (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 ALA 3.7 0.7 - - - +
56A LYS* 3.4 3.5 - - - -
57A VAL* 3.0 54.3 + - + +
59A TRP* 3.7 16.7 - - + -
76A THR* 1.3 75.1 - - - +
78A GLU* 1.3 66.9 + - - +
79A VAL* 5.8 3.4 - - + -
9B LEU* 5.1 7.8 + - - +
150B VAL* 4.8 12.7 - - + +
151B LYS 3.3 12.8 - - - +
152B LEU* 4.4 15.2 - - + +
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Residues in contact with GLU 78 (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* 4.4 8.7 + - - -
54A HIS* 4.0 29.7 + - + +
55A ALA 3.1 9.4 - - - +
56A LYS* 4.2 7.0 - - + -
76A THR* 4.2 15.1 - - + +
77A GLU* 1.3 79.0 - - - +
79A VAL* 1.3 66.3 + - - +
80A GLU* 4.2 2.6 - - + +
201A PO4 5.0 1.7 + - - -
139B LYS* 3.6 27.3 + - - -
149B PRO 4.0 0.2 - - - +
150B VAL* 3.4 5.5 - - - +
151B LYS* 2.8 59.8 + - + +
153B LYS* 3.7 21.1 + - + -
203B PO4 4.5 2.4 + - - -
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Residues in contact with VAL 79 (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* 3.2 4.7 - - - +
55A ALA* 3.0 41.7 + - + +
77A GLU* 5.8 4.7 - - + +
78A GLU* 1.3 78.5 - - - +
80A GLU* 1.3 61.7 + - - +
81A TYR* 3.6 9.6 - - + +
148B LEU* 3.8 31.9 - - + -
149B PRO 3.3 10.1 - - - +
150B VAL* 4.3 19.3 - - + -
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Residues in contact with GLU 80 (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* 3.2 28.1 + - + -
53A GLY 3.8 3.8 - - - +
54A HIS* 3.8 10.8 - - + -
78A GLU* 5.3 3.1 - - + +
79A VAL* 1.3 71.9 - - - +
81A TYR* 1.3 61.6 + - - +
82A PHE 4.1 2.0 - - - +
83A ASN* 3.4 27.4 - - - +
205A PO4 3.4 12.5 + - - -
148B LEU* 3.4 28.6 - - - +
149B PRO* 3.0 31.3 + - + +
151B LYS* 2.6 41.6 + - + +
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Residues in contact with TYR 81 (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 GLY 2.8 9.8 + - - +
54A HIS* 3.8 6.5 - - - -
55A ALA* 3.6 37.3 - - + +
79A VAL* 3.6 15.4 - - + +
80A GLU* 1.3 73.4 - - - +
82A PHE* 1.3 62.3 + - + +
119A PRO* 5.1 2.4 - - - +
123A LEU* 4.2 16.6 - - + +
124A ALA* 3.7 36.1 - - + +
134A VAL* 4.7 5.3 - - + +
136A TYR* 4.1 14.1 - - - +
148B LEU* 3.6 31.9 - - + +
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Residues in contact with PHE 82 (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 ALA* 3.7 23.6 - - + -
52A ARG* 3.3 10.8 - - - +
53A GLY 3.0 36.8 + - - +
80A GLU* 3.6 3.8 - - - +
81A TYR* 1.3 82.7 - - + +
83A ASN* 1.3 72.0 + - - +
84A HIS* 3.7 26.0 - + + -
116A PHE* 3.8 19.5 - + - -
117A GLU 4.0 7.9 - - - -
118A LEU* 3.8 19.1 - - + -
119A PRO* 3.5 37.5 - - + -
123A LEU* 5.1 3.4 - - + -
136A TYR* 4.3 18.4 - + + -
156A PHE* 5.1 2.7 - + - -
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Residues in contact with ASN 83 (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* 2.9 26.9 + - - -
51A ALA 3.4 5.1 - - - +
52A ARG* 3.1 23.2 + - - -
80A GLU* 3.4 11.9 - - - +
82A PHE* 1.3 85.4 - - - +
84A HIS* 1.3 72.0 + - - +
85A LYS* 4.1 10.9 - - - +
205A PO4 3.1 21.3 + - - +
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Residues in contact with HIS 84 (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* 4.1 3.2 - - + +
50A HIS* 3.5 2.1 - - - -
51A ALA* 2.7 40.9 + - + +
82A PHE* 3.7 21.9 - + + -
83A ASN* 1.3 80.7 + - - +
85A LYS* 1.3 82.3 + - - +
86A ASP* 4.3 11.5 + - + +
115A SER 5.1 1.4 + - - -
116A PHE* 3.5 36.6 - + + +
117A GLU 5.6 2.7 + - - -
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Residues in contact with LYS 85 (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 3.5 8.7 - - - +
50A HIS* 3.7 24.7 - - + +
83A ASN* 4.1 12.8 - - - +
84A HIS* 1.3 92.7 + - - +
86A ASP* 1.3 65.7 + - - +
202A PO4 2.7 48.9 + - - +
205A PO4 4.2 6.2 + - - -
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Residues in contact with ASP 86 (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* 3.5 4.0 - - - +
49A ILE* 2.9 53.9 + - + +
84A HIS* 4.3 10.3 + - - +
85A LYS* 1.3 77.9 - - - +
87A ILE* 1.3 82.4 + - - +
88A LEU* 4.7 7.3 - - - +
114A PHE* 6.0 0.3 - - - -
115A SER 4.9 10.4 + - - +
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Residues in contact with ILE 87 (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 LEU 4.0 4.9 - - - +
48A LYS* 4.2 24.2 - - + +
86A ASP* 1.3 90.7 + - - +
88A LEU* 1.3 70.3 + - - +
89A ILE 3.4 15.7 - - - +
90A GLY 3.3 22.0 - - - +
91A HIS* 3.7 29.8 - - + +
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Residues in contact with LEU 88 (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* 3.8 19.7 - - + -
47A LEU* 2.7 32.7 + - + +
49A ILE* 3.7 32.3 - - + -
86A ASP* 4.7 9.2 - - - +
87A ILE* 1.3 82.4 - - - +
89A ILE* 1.3 63.9 + - + +
112A TYR* 3.9 24.2 - - + +
113A ALA 3.4 20.6 - - - +
114A PHE* 4.1 13.2 - - + -
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Residues in contact with ILE 89 (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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36A LEU* 6.0 0.4 - - + -
44A VAL* 4.3 15.9 - - + +
45A LYS 5.1 0.2 - - - +
46A SER* 3.2 8.2 - - - -
47A LEU* 3.1 48.4 + - + +
87A ILE* 3.4 5.4 - - - +
88A LEU* 1.3 85.1 - - - +
90A GLY* 1.3 72.3 + - - +
103A HIS* 4.0 34.5 - - + +
105A ILE* 4.5 11.2 - - + -
112A TYR* 3.6 41.1 - - + +
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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