Contacts of the strand formed by residues 56 - 66 (chain B) in PDB entry 6I53
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 ASP 56 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49B MET* 4.7 0.4 - - - +
50B VAL* 3.7 4.3 - - - +
51B SER* 3.0 39.7 + - - +
54B ASN* 3.3 29.7 - - - +
55B MET* 1.3 75.4 - - - +
57B TYR* 1.3 65.3 + - - +
58B THR* 5.9 0.2 - - - -
102B LYS* 3.8 16.5 + - - +
133B THR* 3.3 24.7 - - + +
134B ALA 3.3 14.6 - - - +
135B ALA* 4.1 2.2 - - - -
136B CYS* 3.8 6.2 - - - +
138B MET* 4.5 0.5 - - - +
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Residues in contact with TYR 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 4.5 11.9 - - + -
49B MET 3.3 12.1 - - - +
50B VAL* 4.1 19.1 - - + -
56B ASP* 1.3 75.6 - - - +
58B THR* 1.3 62.8 + - - +
59B LEU* 3.7 33.8 - - + +
132B THR 3.7 0.2 - - - +
133B THR* 3.3 3.8 - - - -
134B ALA* 2.8 64.9 + - + +
135B ALA 4.4 2.0 - - - -
136B CYS* 3.5 17.9 - - - -
150B CYS* 3.9 17.4 + - + -
151B THR 2.4 36.5 + - - -
152B LEU* 3.5 13.9 - - - +
212B PHE* 4.9 11.3 - + - -
214B LEU* 5.9 1.8 - - + -
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Residues in contact with THR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.4 8.1 - - - +
48B ASP* 2.9 59.5 + - + +
49B MET* 3.1 25.9 + - + +
56B ASP* 5.9 0.2 - - - -
57B TYR* 1.3 74.6 - - - +
59B LEU* 1.3 62.0 + - - +
131B THR* 3.9 16.6 - - + -
132B THR 3.4 9.2 - - - +
133B THR* 3.8 20.1 + - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 3.7 31.0 - - + -
46B SER 4.0 0.4 - - - +
47B ILE* 3.7 27.6 - - + -
57B TYR* 3.7 26.7 - - + +
58B THR* 1.3 74.5 - - - +
60B THR* 1.3 63.0 + - - +
61B MET* 4.0 17.2 - - - +
130B ILE 3.5 2.3 - - - +
131B THR* 3.3 1.7 - - - -
132B THR* 2.7 49.5 + - + +
152B LEU* 3.7 30.1 - - + -
210B LEU* 5.3 0.9 - - + -
212B PHE* 5.0 8.5 - - + -
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.7 3.1 - - - +
45B ALA* 2.8 37.2 + - + -
46B SER* 3.0 24.7 + - - +
48B ASP* 3.5 14.2 + - - -
59B LEU* 1.3 70.7 - - - +
61B MET* 1.3 66.5 + - - +
107B HIS* 4.1 9.4 - - + +
129B ARG* 4.6 17.5 - - + +
130B ILE 3.4 4.9 - - - +
131B THR* 3.1 32.3 + - - +
116C SER 5.0 3.4 - - - +
117C LYS* 5.6 4.2 - - - +
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Residues in contact with MET 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ILE* 3.7 27.8 - - + -
43B ASP 3.4 10.3 - - - +
44B ILE* 3.9 11.0 - - + -
45B ALA* 3.9 1.8 - - - +
59B LEU* 4.0 20.6 - - + +
60B THR* 1.3 77.7 - - - +
62B TYR* 1.3 64.7 + - - +
63B PHE* 3.7 17.0 + - + -
98B PHE* 3.6 37.7 - - + -
128B LEU 3.6 0.2 - - - +
129B ARG* 3.5 6.1 - - - +
130B ILE* 3.0 40.9 + - + +
132B THR* 4.5 12.3 - - + -
152B LEU* 3.9 14.1 - - + -
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ASN 3.5 3.3 - - - +
42B ILE* 3.4 4.8 - - - -
43B ASP* 2.6 73.7 + - + +
45B ALA* 4.2 20.0 - - + +
61B MET* 1.3 72.5 - - - +
63B PHE* 1.3 58.0 + - - +
64B GLN* 3.7 14.9 + - - +
128B LEU 3.4 3.8 - - - +
129B ARG* 3.7 29.4 + - + -
112C PHE* 3.3 31.1 - + - -
114C ARG* 3.4 36.3 + - + +
172C TYR* 3.8 23.3 - + - +
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A THR* 4.6 3.4 - - + -
40B MET* 3.6 32.3 - - + -
41B ASN 3.8 1.1 - - - -
42B ILE* 3.6 23.3 - - + +
61B MET* 3.7 16.8 + - + -
62B TYR* 1.3 71.2 - - - +
64B GLN* 1.3 61.3 + - - +
65B GLN* 3.3 28.3 - - + -
96B THR* 3.9 6.7 - - - -
98B PHE* 4.4 9.4 - + - -
126B TYR 3.6 2.8 - - - +
127B GLY* 3.6 1.6 - - - -
128B LEU* 2.7 42.5 + - + +
130B ILE* 3.9 31.4 - - + -
154B ILE* 3.9 32.3 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLY 4.6 0.2 - - - -
40B MET* 3.4 5.4 - - - +
41B ASN* 2.8 50.1 + - + +
43B ASP* 6.0 3.4 - - - +
62B TYR* 4.4 17.3 - - - +
63B PHE* 1.3 78.5 - - - +
65B GLN* 1.3 65.7 + - - +
66B TYR* 5.0 6.5 + - + -
115B MET* 4.9 5.9 - - - -
125B LEU* 3.8 23.7 - - + +
126B TYR 3.7 3.6 - - - -
127B GLY* 4.0 9.6 - - - -
172C TYR* 5.2 3.9 + - - +
215C THR* 5.4 3.8 + - - -
216C THR* 4.3 20.7 - - - +
217C SER* 3.6 27.6 + - - +
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Residues in contact with GLN 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A THR* 5.1 1.8 + - - +
38B VAL* 4.2 9.9 - - + -
39B GLY 3.4 4.7 - - - -
40B MET* 3.9 14.4 - - + +
63B PHE* 3.3 21.7 - - + -
64B GLN* 1.3 81.6 - - - +
66B TYR* 1.3 62.1 + - - +
67B TRP* 3.7 15.1 - - + -
94B PRO* 3.4 28.9 + - - +
96B THR* 3.0 39.9 + - - +
124B VAL 3.2 5.7 - - - +
125B LEU* 3.5 2.9 - - - -
126B TYR* 3.1 42.6 + - - +
128B LEU* 5.9 0.6 - - - +
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Residues in contact with TYR 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B CYS 3.7 1.2 - - - +
38B VAL* 3.3 4.5 - - - -
39B GLY 2.7 41.8 + - - +
41B ASN* 5.9 4.7 - - + -
64B GLN* 5.0 6.8 + - + -
65B GLN* 1.3 82.0 - - - +
67B TRP* 1.3 62.1 + - - +
119B HIS* 5.3 7.3 + - - -
123B THR* 4.7 17.0 - - + -
124B VAL 3.4 4.3 - - - +
125B LEU* 3.5 44.7 - - + +
167B TYR* 4.8 3.0 + - - +
169B ARG* 3.3 51.4 - - - +
216C THR* 4.9 17.3 + - + +
217C SER* 5.2 2.8 - - - -
1K NAG 5.2 8.5 + - - -
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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