Contacts of the strand formed by residues 56 - 67 (chain C) in PDB entry 6D6Q
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 THR 56 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C ARG* 3.0 13.8 + - - +
52C LYS* 3.1 5.2 - - - +
53C LEU* 2.9 35.3 + - + -
55C ASN* 1.3 74.1 - - - +
57C THR* 1.3 77.1 + - - +
143C ASP 3.3 14.6 - - - +
144C TYR* 5.2 0.2 - - - -
145C ASP* 3.4 4.9 - - - +
146C GLY 2.9 37.4 + - - +
147C ASN 4.3 6.5 - - - +
148C ILE* 4.3 16.6 - - + -
151C ALA* 4.5 9.2 - - + -
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Residues in contact with THR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.0 19.5 - - + -
51C VAL 3.4 12.1 - - - +
52C LYS* 3.8 15.5 - - + +
55C ASN 3.4 9.0 + - - -
56C THR* 1.3 81.8 + - - +
58C VAL* 1.3 76.6 + - - +
141C CYS* 3.8 6.4 - - - -
142C LEU* 3.4 43.6 + - + -
143C ASP* 3.4 14.5 + - - -
148C ILE* 4.1 0.3 - - - +
151C ALA* 5.8 0.2 - - - -
45F LEU* 5.9 0.9 - - - +
46F LEU* 5.5 0.8 - - + +
638J PHE* 4.5 12.3 - - + -
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ALA 4.7 0.2 - - - -
50C LEU* 3.3 8.2 - - - +
51C VAL* 2.9 32.8 + - + +
57C THR* 1.3 89.3 - - - +
59C ILE* 1.3 71.0 + - - +
139C LEU* 4.5 6.1 - - + -
140C ILE 3.4 15.9 - - - +
141C CYS* 4.6 0.9 - - - -
142C LEU* 5.3 0.4 - - - -
148C ILE* 3.4 26.2 - - + -
151C ALA* 3.4 26.9 - - + +
152C CYS* 4.2 19.5 - - - +
155C ALA* 4.1 17.7 - - + -
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Residues in contact with ILE 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ILE* 3.8 26.7 - - + -
49C ALA 3.3 14.4 - - - +
50C LEU* 3.9 19.1 - - + -
58C VAL* 1.3 81.9 - - - +
60C CYS* 1.3 69.2 + - - +
138C ASP 3.7 1.6 - - - +
139C LEU* 3.4 1.0 - - - -
140C ILE* 2.9 48.7 + - + +
142C LEU* 4.4 14.1 - - + -
105F PHE* 4.3 17.0 - - + -
151F LEU* 4.5 11.9 - - + -
637J LEU* 4.4 18.8 - - + -
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Residues in contact with CYS 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ILE* 5.6 0.3 - - - +
47C GLY 3.9 0.2 - - - +
48C SER* 3.4 5.7 - - - -
49C ALA 2.9 32.0 + - - +
59C ILE* 1.3 78.6 - - - +
61C GLY* 1.3 68.5 + - - +
62C VAL* 4.6 2.0 - - - -
137C CYS* 4.3 7.0 - - - -
138C ASP 3.4 5.2 - - - -
139C LEU* 3.8 30.3 - - + +
155C ALA* 3.9 23.3 - - + +
156C LEU* 4.2 17.5 - - - -
159C ALA* 4.1 15.6 - - + +
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Residues in contact with GLY 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 4.8 0.9 - - - -
47C GLY 3.4 7.0 - - - -
48C SER* 4.7 1.6 - - - -
60C CYS* 1.3 75.8 - - - +
62C VAL* 1.3 60.9 + - - -
63C LYS 4.0 0.3 + - - -
136C TYR 3.5 2.6 - - - +
138C ASP* 2.9 37.4 + - - +
105F PHE* 3.7 34.0 - - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C ALA* 4.7 0.4 - - - +
46C ASP* 3.3 10.0 + - - +
47C GLY* 2.9 50.4 + - - +
60C CYS* 4.2 5.1 - - - -
61C GLY* 1.3 71.5 - - - -
63C LYS* 1.3 69.0 + - - +
135C LEU* 4.1 23.8 - - + -
136C TYR 3.3 9.0 - - - +
137C CYS* 4.1 18.2 - - + +
156C LEU* 6.3 0.2 - - + -
159C ALA* 4.2 11.7 - - + +
160C LEU* 4.9 12.1 - - + +
163C VAL* 4.2 15.0 - - + -
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Residues in contact with LYS 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C THR 2.5 26.2 + - - +
45C ALA* 3.8 23.5 - - + +
46C ASP* 3.7 8.7 + - - +
61C GLY 5.2 0.2 - - - +
62C VAL* 1.3 75.8 - - - +
64C ALA* 1.3 66.2 + - - +
65C GLU* 5.4 3.4 - - + -
134C VAL 3.7 0.2 - - - +
135C LEU* 3.4 6.7 - - - +
136C TYR* 2.9 37.1 + - + +
138C ASP* 5.5 1.3 - - - +
104F PRO 4.2 7.0 - - - +
105F PHE* 4.0 23.8 - - + +
107F GLY 3.2 19.6 + - - -
108F ARG* 3.6 15.6 + - - +
109F ARG 4.8 8.7 - - - -
110F ARG* 4.6 20.0 - - + +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C ASP* 2.9 22.5 + - + +
63C LYS* 1.3 78.6 - - - +
65C GLU* 1.3 70.2 + - - +
133C TRP* 3.8 16.4 - - + -
134C VAL 3.6 3.6 - - - -
135C LEU* 4.1 7.2 - - + -
165C LEU* 3.6 27.6 - - + -
166C PRO* 5.8 0.9 - - + -
16F PRO* 5.2 0.2 - - - +
17F PRO* 3.7 14.8 - - + +
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Residues in contact with GLU 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C LYS* 5.4 3.3 - - + -
64C ALA* 1.3 82.1 - - - +
66C PHE* 1.3 68.3 + - - +
133C TRP* 3.4 10.5 - - - -
134C VAL* 2.9 41.2 + - + -
136C TYR* 3.4 11.9 - - + -
14F SER* 2.5 41.1 + - - +
15F GLN 3.8 5.8 - - - +
16F PRO* 4.0 20.0 - - + +
17F PRO* 4.4 5.2 - - - -
109F ARG* 5.1 0.7 - - - +
110F ARG* 3.1 39.1 + - + +
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Residues in contact with PHE 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C GLU* 1.3 82.4 - - - +
67C ALA* 1.3 66.5 + - - +
126C ILE* 4.7 9.2 - - + -
131C LEU* 4.3 29.4 - - + -
132C VAL 3.8 5.4 - - - +
133C TRP* 3.4 36.8 - + - -
134C VAL* 4.4 0.2 - - - -
168C VAL* 3.6 25.6 - - + -
177C ALA* 5.6 4.9 - - + -
179C VAL* 4.1 7.0 - - + -
14F SER* 3.2 23.7 - - - -
15F GLN* 3.0 13.8 + - + +
16F PRO* 4.4 0.9 - - - +
17F PRO* 3.5 34.5 - - + -
20F TYR* 4.2 24.2 - + + -
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Residues in contact with ALA 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C PHE* 1.3 79.7 - - - +
68C ALA* 1.3 61.2 + - - +
78C TYR* 5.0 4.9 - - + -
130C LYS 4.7 0.7 - - - -
131C LEU* 3.5 7.9 - - - +
132C VAL* 2.8 39.6 + - - +
134C VAL* 4.4 9.0 - - + -
11F PRO* 4.2 22.9 - - + -
13F GLU 3.9 17.9 - - - +
14F SER* 4.3 2.0 - - - +
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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