Contacts of the strand formed by residues 61 - 72 (chain S) in PDB entry 5DM6
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 61 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53S ASP* 4.9 9.5 - - - +
54S ILE 3.3 4.7 - - - -
55S THR* 3.5 31.4 - - + +
59S GLY 3.5 15.9 - - - +
60S GLU* 1.3 69.9 - - - +
62S PHE* 1.3 68.3 + - - +
63S PRO* 4.3 4.2 - - - +
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Residues in contact with PHE 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ASN* 4.9 17.0 - - - -
53S ASP* 4.6 1.3 - - - -
54S ILE* 2.9 38.5 + - - +
56S VAL* 5.8 5.4 - - + -
60S GLU* 3.4 47.3 - - + -
61S THR* 1.3 79.5 + - - +
63S PRO* 1.3 71.3 - - + +
85S MET* 3.6 34.8 - - + +
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Residues in contact with PRO 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S LEU* 4.2 13.0 - - + -
52S PHE 3.6 6.7 - - - +
53S ASP* 4.4 15.9 - - + +
61S THR 4.3 3.6 - - - +
62S PHE* 1.3 87.2 - - + +
64S ALA* 1.3 63.3 + - - +
85S MET* 3.5 8.1 - - - +
86S VAL* 3.1 35.4 + - + +
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Residues in contact with ALA 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23S ALA* 5.4 0.4 - - + -
51S LEU* 3.0 6.7 + - - +
52S PHE 2.9 32.9 + - - +
54S ILE* 3.5 28.3 - - + -
63S PRO* 1.3 75.8 - - - +
65S LEU* 1.3 63.2 + - - +
66S VAL* 5.8 0.2 - - - +
83S PHE* 4.6 8.5 - - + -
84S TYR 3.3 15.5 - - - +
85S MET* 4.0 10.8 - - + -
86S VAL* 3.6 9.6 - - - +
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Residues in contact with LEU 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48S THR 3.6 18.4 - - - +
49S THR* 3.7 15.5 - - - +
50S GLY 4.1 1.1 - - - +
51S LEU* 3.3 37.7 - - + +
64S ALA* 1.3 72.2 - - - +
66S VAL* 1.3 61.9 + - - +
83S PHE* 3.0 10.6 - - - -
84S TYR* 2.8 44.7 + - + +
86S VAL* 3.6 16.8 - - + +
91S PRO* 6.3 3.4 - - + -
92S VAL* 5.7 8.7 - - + -
94S VAL* 5.1 15.5 - - + -
130S ILE* 4.8 14.4 - - + -
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Residues in contact with VAL 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39S PHE* 4.8 5.6 - - + -
43S PHE* 4.3 16.4 - - + -
46S GLN* 6.3 0.4 - - + -
47S SER 3.5 24.7 - - - +
48S THR* 3.2 25.9 + - - +
50S GLY* 4.9 4.7 - - - -
51S LEU 5.5 0.4 - - - +
65S LEU* 1.3 79.2 - - - +
67S LYS* 1.3 63.2 + - - +
68S ALA 4.3 1.6 - - - +
69S VAL* 4.1 26.2 - - + -
81S VAL* 4.3 5.4 - - + -
82S ASP 4.1 5.8 - - - +
83S PHE* 3.5 26.2 - - + -
84S TYR* 5.3 0.4 - - - -
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Residues in contact with LYS 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S TYR* 4.4 2.5 - - - +
26S LYS* 5.2 0.7 - - - +
65S LEU 3.8 1.2 + - - -
66S VAL* 1.3 72.9 - - - +
68S ALA* 1.3 64.8 + - + +
82S ASP* 2.9 17.4 + - + +
83S PHE 4.5 0.7 - - - -
84S TYR* 3.7 38.8 - - + +
92S VAL* 3.8 24.8 - - + +
93S GLU 5.3 3.8 - - - -
121S GLN* 6.1 1.2 - - - +
106Y U 2.9 55.5 + - - +
107Y C 3.5 8.8 + - - +
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Residues in contact with ALA 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J TYR 5.9 1.6 - - - -
66S VAL* 3.8 1.2 - - - +
67S LYS* 1.3 81.2 - - + +
69S VAL* 1.3 72.4 + - - +
81S VAL* 3.7 1.0 - - - +
82S ASP* 2.9 51.1 + - + +
106Y U 5.9 4.0 - - - +
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Residues in contact with VAL 69 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J TYR 5.5 5.5 + - - +
139J ASP* 4.0 26.0 - - - +
39S PHE* 4.0 3.8 - - + -
43S PHE* 3.4 39.5 - - + -
66S VAL* 4.1 6.7 - - + -
68S ALA* 1.3 83.6 - - - +
70S GLN* 1.3 64.2 + - - +
71S MET* 3.8 30.5 + - + +
78S PRO* 4.8 5.2 - - + -
80S HIS 3.9 7.0 - - - +
81S VAL* 3.8 19.1 - - + +
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Residues in contact with GLN 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139J ASP* 5.4 0.9 - - - -
69S VAL* 1.3 76.2 - - - +
71S MET* 1.3 64.7 + - - +
78S PRO* 3.9 1.0 - - - +
79S ILE* 3.0 38.2 + - + +
80S HIS* 2.9 36.9 + - + +
77Y G 4.2 6.9 - - - +
78Y A 2.6 50.6 + - - -
79Y U 3.3 22.2 + - - +
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Residues in contact with MET 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26J ASP* 4.6 12.3 - - - +
137J VAL* 4.2 23.6 - - + -
139J ASP* 4.4 21.2 + - - +
69S VAL* 3.8 21.5 - - + +
70S GLN* 1.3 81.5 - - - +
72S ASP* 1.3 68.6 + - - +
73S LYS* 3.6 10.0 + - - +
76S ARG* 5.0 5.8 - - - -
77S ALA* 3.4 14.1 - - - +
78S PRO* 3.2 45.3 - - + -
79S ILE* 3.6 12.4 - - - +
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Residues in contact with ASP 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J ASP* 5.2 1.6 - - - +
71S MET* 1.3 73.9 - - - +
73S LYS* 1.3 63.0 + - - +
74S ARG* 3.4 14.9 + - - +
75S LYS* 3.6 33.2 + - + +
76S ARG* 2.7 32.3 + - - +
77S ALA* 2.8 18.0 + - + +
79S ILE* 3.9 23.9 - - + +
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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