Contacts of the strand formed by residues 56 - 69 (chain D) in PDB entry 4COF
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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D MET* 5.4 3.8 - - - +
50D VAL* 3.7 0.7 - - - -
51D SER* 2.8 45.1 + - - +
54D ASN* 3.3 16.7 - - - +
55D MET* 1.3 76.9 - - - +
57D TYR* 1.4 58.9 + - - +
58D THR* 5.2 1.0 + - - -
102D LYS* 3.0 37.4 + - + +
133D THR* 3.7 17.8 - - + +
134D ALA 3.0 20.6 - - - +
136D CYS* 3.8 7.1 + - - +
138D MET* 4.3 2.8 - - - +
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Residues in contact with TYR 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 4.3 10.8 - - + -
49D MET* 3.3 14.1 - - - +
50D VAL* 4.0 17.0 - - + -
51D SER 4.7 0.2 - - - +
56D ASP* 1.4 75.6 - - - +
58D THR* 1.3 63.5 + - - +
59D LEU* 3.9 30.7 - - + -
132D THR 3.7 0.5 - - - +
133D THR* 3.4 3.2 - - - -
134D ALA* 2.9 59.4 + - + +
135D ALA 4.1 5.4 - - - -
136D CYS* 3.8 7.9 - - + -
150D CYS* 3.7 32.8 - - + -
151D THR* 2.6 32.0 + - - -
152D LEU* 3.7 10.9 + - - +
212D PHE* 4.4 13.4 - + - -
214D LEU* 5.8 0.9 - - + -
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.5 10.6 - - - +
48D ASP* 3.1 33.9 + - + +
49D MET* 2.8 33.1 + - - +
56D ASP* 5.2 0.5 + - - -
57D TYR* 1.3 72.6 - - - +
59D LEU* 1.3 63.3 + - - +
131D THR* 3.7 24.5 - - + -
132D THR 3.3 7.4 - - - +
133D THR* 3.0 27.7 + - - +
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Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE* 3.5 39.3 - - + -
46D SER 3.5 5.8 - - - -
47D ILE* 3.8 14.8 - - + +
48D ASP* 4.1 1.1 - - - -
57D TYR* 3.9 17.0 - - + +
58D THR* 1.3 75.0 - - - +
60D THR* 1.4 62.9 + - - +
61D MET* 3.7 29.6 - - + -
130D ILE 3.8 1.0 - - - +
131D THR* 3.4 2.8 - - - +
132D THR* 2.8 37.5 + - - +
152D LEU* 4.0 24.5 - - + -
210D LEU* 5.9 0.2 - - + -
212D PHE* 4.2 14.1 - - + -
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Residues in contact with THR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ILE* 3.9 2.9 - - - +
45D ALA* 2.9 28.0 + - + -
46D SER* 3.0 23.5 + - - +
48D ASP* 2.8 25.3 + - - -
59D LEU* 1.4 71.2 - - - +
61D MET* 1.3 66.0 + - - +
107D HIS* 3.7 12.7 - - + +
129D ARG* 4.0 24.0 - - + +
130D ILE 3.3 7.4 - - - +
131D THR* 3.0 25.3 + - - +
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Residues in contact with MET 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D ILE* 3.8 30.5 - - + -
43D ASP 3.5 12.1 - - - +
44D ILE* 4.3 6.3 - - + -
45D ALA* 4.0 2.7 - - - +
59D LEU* 3.7 20.2 - - + -
60D THR* 1.3 77.2 - - - +
62D TYR* 1.3 67.0 + - - +
63D PHE* 4.5 6.3 - - + +
98D PHE* 3.6 31.4 - - + -
128D LEU 3.6 0.7 - - - +
129D ARG* 3.3 7.6 - - - +
130D ILE* 2.9 47.0 + - + +
132D THR* 3.7 21.5 - - - +
152D LEU* 3.9 16.8 - - + -
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Residues in contact with TYR 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN 3.7 1.2 - - - +
42D ILE* 3.4 6.8 - - - +
43D ASP* 3.0 61.3 + - + +
45D ALA* 4.1 20.3 - - + +
61D MET* 1.3 73.1 - - - +
63D PHE* 1.3 59.9 + - - +
64D GLN* 3.8 14.5 + - + +
128D LEU 3.6 5.2 - - - +
129D ARG* 3.7 38.1 + - + -
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Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR* 3.9 20.4 - - + -
40D MET* 3.5 32.3 - - + -
41D ASN 3.9 0.7 - - - -
42D ILE* 3.8 31.2 - - + -
61D MET* 3.8 10.0 + - + -
62D TYR* 1.3 69.6 - - - +
64D GLN* 1.3 61.2 + - - +
65D GLN* 3.6 32.7 + - + -
96D THR* 3.7 17.3 - - + -
98D PHE* 3.9 21.3 - + - -
126D TYR 3.6 1.9 - - - +
127D GLY* 3.4 2.1 - - - -
128D LEU* 2.7 44.7 + - + +
130D ILE* 3.7 16.8 - - + -
154D ILE* 4.3 5.6 - - + -
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Residues in contact with GLN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLY 3.7 0.7 - - - +
40D MET* 3.4 4.9 - - - +
41D ASN* 2.8 52.8 + - + +
62D TYR* 4.5 16.6 - - + +
63D PHE* 1.3 77.9 - - - +
65D GLN* 1.3 62.4 + - - +
66D TYR* 2.7 40.6 + - + -
115D MET* 4.2 18.0 - - - +
125D LEU* 3.7 12.2 - - + +
126D TYR 3.4 3.1 - - - -
127D GLY* 4.5 7.0 - - - -
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Residues in contact with GLN 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C THR* 4.4 11.7 + - - +
38D VAL* 3.9 10.3 - - + -
39D GLY 3.6 4.0 - - - -
40D MET* 3.6 13.1 - - + +
63D PHE* 3.6 33.2 + - + -
64D GLN* 1.3 78.7 - - - +
66D TYR* 1.3 63.4 + - - +
67D TRP* 4.0 9.8 - - + -
94D PRO* 3.6 16.2 + - - +
96D THR* 2.7 26.0 + - - -
124D VAL 3.6 1.2 - - - +
125D LEU* 3.6 3.1 - - - +
126D TYR* 2.8 62.9 + - + +
128D LEU* 4.7 1.8 - - - +
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Residues in contact with TYR 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D CYS 3.5 2.1 - - - +
38D VAL* 3.4 3.1 - - - +
39D GLY* 2.7 54.9 + - - +
41D ASN* 3.9 15.0 + - + -
64D GLN* 2.7 32.8 + - + -
65D GLN* 1.3 76.3 - - - +
67D TRP* 1.3 60.3 + - - +
119D HIS* 5.6 4.9 - + - -
123D THR* 6.3 1.6 - - - -
124D VAL 3.2 7.4 - - - +
125D LEU* 3.1 43.5 - - + +
167D TYR* 4.5 4.6 + - - +
169D ARG* 3.2 55.5 + - + -
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Residues in contact with TRP 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PRO* 4.0 14.5 - - + +
36D VAL* 4.0 10.8 - - + -
37D CYS 3.8 15.0 - - - +
38D VAL* 4.1 11.9 - - + -
65D GLN* 4.0 9.9 - - + -
66D TYR* 1.3 77.9 - - - +
68D ARG* 1.3 71.3 + - - +
69D ASP* 4.1 9.5 + - - +
72D LEU* 6.2 0.2 - - + -
91D LEU* 5.9 1.6 - - + -
92D TRP* 3.3 42.3 + + - -
93D VAL* 3.9 12.3 - - + -
94D PRO* 3.7 28.5 - - + -
116D ILE* 5.3 0.4 - - + -
123D THR* 3.2 7.0 - - - -
124D VAL* 2.6 63.9 + - + +
126D TYR* 3.5 33.7 - + + -
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Residues in contact with ARG 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D PRO* 3.4 17.3 - - - +
36D VAL* 4.0 8.1 - - + +
37D CYS 4.8 1.0 + - - -
67D TRP* 1.3 77.2 - - - +
69D ASP* 1.3 61.4 + - - +
70D LYS* 4.0 37.4 + - + +
121D ASP* 3.2 45.1 + - - +
122D GLY 3.7 9.0 - - - -
123D THR* 3.8 13.0 - - + +
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR* 2.8 33.6 + - - -
29D PRO* 3.7 21.9 - - + +
67D TRP* 4.1 10.4 + - - +
68D ARG* 1.3 72.6 - - - +
70D LYS* 1.3 57.5 + - - +
71D ARG* 2.9 32.8 + - - +
72D LEU* 2.9 41.3 + - + +
92D TRP* 5.0 1.2 - - - +
122D GLY* 2.7 28.1 + - - +
124D VAL* 4.5 1.1 - - + -
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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
------------------------------------------------------------
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