Contacts of the strand formed by residues 66 - 76 (chain A) in PDB entry 4IQJ
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 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A PRO 3.0 16.7 + - - +
41A ALA* 3.5 9.5 - - + +
42A LEU 3.2 24.3 + - - +
64A GLY 4.1 1.0 + - - -
65A VAL* 1.3 72.1 - - - +
67A PRO* 1.3 74.4 - - + +
68A ILE* 4.5 2.3 - - + +
278A ALA 2.7 28.6 + - - +
279A ARG* 2.8 24.5 + - - +
281A CYS* 3.3 27.9 + - - +
282A ASP* 4.3 6.3 - - - +
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Residues in contact with PRO 67 (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 LEU 3.6 4.7 - - - +
56A PHE* 3.4 26.2 - - + -
57A TYR* 3.5 46.7 - - + +
60A ALA* 3.8 9.4 - - + -
61A THR* 4.7 6.5 - - - +
65A VAL 3.4 8.7 - - - +
66A LYS* 1.3 95.9 - - + +
68A ILE* 1.3 64.3 + - - +
69A ILE* 4.1 3.8 + - + +
281A CYS 4.6 6.2 - - - +
283A VAL* 5.3 6.5 + - - +
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Residues in contact with ILE 68 (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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9A HIS 5.5 0.2 - - - +
10A LEU* 3.6 27.1 - - + -
41A ALA* 4.7 4.7 - - + -
42A LEU 3.0 15.5 + - - +
43A ALA* 3.2 18.2 - - + -
44A MET* 3.1 19.8 + - - +
56A PHE* 4.0 1.9 - - - -
66A LYS* 4.5 5.4 - - + +
67A PRO* 1.3 77.2 - - - +
69A ILE* 1.3 61.3 + - - +
70A GLY 3.1 8.7 + - - -
99A LEU* 4.0 18.4 - - + -
100A ALA 4.6 3.8 - - - +
278A ALA* 3.7 29.6 - - + +
281A CYS* 3.8 33.7 - - + +
283A VAL* 6.2 2.0 - - - -
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Residues in contact with ILE 69 (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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44A MET* 4.5 5.2 - - + +
50A LEU* 3.8 26.7 - - + -
53A ALA* 4.1 23.3 - - + +
56A PHE* 5.4 6.1 - - + -
57A TYR* 4.9 9.4 - - + -
67A PRO* 4.1 2.4 + - + -
68A ILE* 1.3 71.5 - - - +
70A GLY* 1.3 60.0 + - - +
100A ALA* 3.1 36.9 + - + +
106A TYR* 3.9 28.3 - - + -
109A LEU* 3.3 9.6 - - + +
283A VAL* 4.7 12.6 - - + +
285A LEU* 3.8 32.5 - - + -
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Residues in contact with GLY 70 (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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44A MET* 2.8 28.6 + - - +
45A THR* 3.8 10.7 - - - -
46A ASP 4.9 0.7 + - - -
49A ASN 5.0 0.3 - - - +
50A LEU* 3.5 19.9 - - - +
68A ILE 3.1 3.2 + - - -
69A ILE* 1.3 75.0 - - - +
71A TYR* 1.3 64.6 + - - +
98A LEU 3.2 12.1 - - - -
99A LEU* 4.0 5.8 - - - -
109A LEU* 4.5 1.3 - - - -
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Residues in contact with TYR 71 (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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45A THR* 4.0 6.4 - - - +
46A ASP 4.3 3.4 - - - +
48A GLY* 3.7 15.8 - - - -
49A ASN* 3.3 43.7 - - - -
50A LEU* 4.7 7.2 - - + -
70A GLY* 1.3 75.9 - - - +
72A GLU* 1.3 58.8 + - - +
73A ALA* 3.1 34.2 + - + -
98A LEU* 2.8 36.3 + - + +
109A LEU* 3.9 30.5 - - + -
112A LEU* 4.0 10.6 + - + -
113A ALA* 3.6 27.4 - - + -
116A ALA* 3.6 26.2 - - - +
125A PRO 4.6 1.7 + - - -
127A ILE* 4.4 3.4 - - + +
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Residues in contact with GLU 72 (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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11A HIS* 2.3 44.4 + - + +
13A HIS* 2.6 25.2 + - + -
45A THR* 4.3 8.9 - - - +
46A ASP 3.2 23.2 + - - +
47A HIS* 3.9 9.2 + - - +
48A GLY 3.3 18.7 + - - -
71A TYR* 1.3 67.8 - - - +
73A ALA* 1.3 63.1 + - - +
74A TYR* 3.6 2.9 + - - -
95A HIS* 2.8 37.1 + - + +
96A LEU 3.4 17.5 - - - +
97A THR* 4.3 2.5 - - - +
145A CYS* 3.8 8.3 + - - -
212A ASP* 4.5 1.0 - - - +
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Residues in contact with ALA 73 (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 GLY 5.0 0.2 - - - +
71A TYR* 3.1 36.7 + - + -
72A GLU* 1.3 72.4 - - - +
74A TYR* 1.3 60.8 + - - +
75A VAL* 3.5 4.9 + - + +
94A PHE 3.4 3.3 - - - +
95A HIS* 3.5 2.3 - - - -
96A LEU* 2.8 37.8 + - + +
98A LEU* 4.1 12.1 - - + -
127A ILE* 3.9 23.1 - - + -
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Residues in contact with TYR 74 (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 HIS* 3.3 33.7 + - + +
48A GLY* 3.9 25.5 - - - -
71A TYR* 5.2 0.6 + - - -
72A GLU 4.8 1.3 - - - -
73A ALA* 1.3 71.1 - - - +
75A VAL* 1.3 55.1 + - - +
93A TYR* 3.4 32.5 - + + -
94A PHE 3.2 1.6 - - - +
95A HIS* 3.5 32.2 - + - -
124A LYS* 3.6 41.4 - - + -
125A PRO* 3.5 25.4 + - + +
126A ARG* 3.1 13.8 - - + -
127A ILE* 2.7 34.5 + - - +
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Residues in contact with VAL 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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73A ALA* 3.8 3.4 - - + +
74A TYR* 1.3 71.1 - - - +
76A ALA* 1.3 75.6 + - - +
93A TYR* 3.3 1.7 - - - -
94A PHE* 2.3 62.3 + - + +
96A LEU* 3.4 40.2 - - + -
127A ILE* 3.5 21.5 - - + +
129A ARG* 4.4 20.0 - - + +
149A GLU* 3.8 21.8 - - - +
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Residues in contact with ALA 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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74A TYR 3.8 1.2 + - - -
75A VAL* 1.3 85.6 - - - +
77A ALA* 1.3 66.1 + - - +
78A GLU* 3.3 2.3 + - - +
79A SER 3.5 20.4 - - - +
80A ARG* 4.1 4.3 - - - +
92A GLY 4.5 7.0 - - - -
93A TYR* 4.5 0.2 - - - +
94A PHE* 4.9 1.3 - - - -
126A ARG* 4.3 17.5 - - + +
127A ILE 2.7 12.4 + - - +
128A ASP* 3.3 25.0 - - - +
129A ARG* 3.7 9.0 + - - -
149A GLU* 4.9 1.6 - - - +
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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