Contacts of the helix formed by residues 71 - 89 (chain B) in PDB entry 5D4P
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 PRO 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU* 3.7 13.9 - - + -
33B VAL* 6.1 1.3 - - - -
69B ALA 4.7 0.2 - - - +
70B VAL* 1.3 97.9 - - + +
72B GLU* 1.3 67.1 + - - +
73B GLU* 3.3 22.2 - - - +
74B LEU* 3.1 44.4 + - + +
75B VAL 3.7 0.3 + - - -
106B PHE* 3.3 25.6 - - + +
107B ARG* 3.8 25.8 - - + +
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Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 5.1 3.4 - - - +
10B LYS* 3.6 45.4 + - + +
70B VAL 3.6 1.2 + - - -
71B PRO* 1.3 71.2 - - - +
73B GLU* 1.3 67.7 + - - +
75B VAL* 3.0 21.3 + - + +
76B GLY 4.4 1.6 + - - -
107B ARG* 5.0 1.8 - - - +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PRO* 3.3 13.8 - - - +
72B GLU* 1.3 84.6 + - - +
74B LEU* 1.3 74.1 + - + +
75B VAL 3.4 0.2 - - - -
76B GLY 4.4 0.6 + - - -
77B PRO* 3.5 17.8 - - - +
107B ARG* 3.5 29.0 + - - +
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Residues in contact with LEU 74 (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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31B ALA* 3.8 26.6 - - + +
32B GLY 4.0 19.3 - - - +
33B VAL* 4.1 15.0 - - + -
70B VAL* 4.5 5.4 - - + -
71B PRO* 3.1 34.5 + - + +
72B GLU 3.0 0.8 - - - -
73B GLU* 1.3 96.5 - - + +
75B VAL* 1.3 65.1 + - - +
76B GLY 3.4 0.7 - - - -
77B PRO* 3.5 8.6 - - + +
78B LEU* 3.1 28.0 + - + +
106B PHE 5.6 0.7 - - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 4.8 7.2 - - + -
10B LYS* 3.7 31.2 - - + -
12B LEU* 4.5 7.4 - - + -
70B VAL* 3.7 21.1 - - + -
71B PRO 3.8 0.9 - - - +
72B GLU* 3.0 16.2 + - + +
74B LEU* 1.3 78.2 - - - +
76B GLY* 1.3 64.3 + - - +
78B LEU* 3.2 6.2 + - - +
79B LEU* 2.9 45.9 + - + +
95B VAL* 4.6 16.2 - - + -
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ALA* 6.4 1.1 - - - -
4A ILE* 4.5 11.4 - - - +
72B GLU 4.4 2.2 + - - -
73B GLU 4.4 0.6 + - - -
75B VAL* 1.3 80.0 - - - +
77B PRO* 1.3 63.7 - - - +
79B LEU* 3.3 6.5 + - - +
80B GLU* 3.0 36.2 + - - +
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Residues in contact with PRO 77 (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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27B LEU* 5.7 0.9 - - - +
31B ALA* 5.9 5.8 - - + -
73B GLU 3.5 18.4 - - - +
74B LEU* 3.5 13.0 - - + +
76B GLY* 1.3 91.1 - - - +
78B LEU* 1.3 56.3 + - - +
80B GLU* 3.3 12.8 + - + +
81B GLY* 3.0 23.9 + - - -
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Residues in contact with LEU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.7 31.4 - - + -
27B LEU* 4.2 16.9 - - + +
28B LEU* 4.0 19.3 - - + -
31B ALA* 3.5 30.0 - - + +
33B VAL* 3.8 21.8 - - + -
70B VAL* 4.1 13.7 - - + -
74B LEU* 3.1 25.2 + - + +
75B VAL* 3.5 4.5 - - - +
77B PRO* 1.3 74.3 - - - +
79B LEU* 1.3 66.0 + - - +
81B GLY* 3.1 3.6 + - - -
82B PHE* 2.9 32.0 + - + -
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Residues in contact with LEU 79 (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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4A ILE* 4.8 13.9 - - + +
6A LEU* 3.7 31.9 - - + -
12B LEU* 5.1 8.1 - - + -
75B VAL* 2.9 37.8 + - + +
76B GLY* 3.8 5.2 - - - +
78B LEU* 1.3 76.7 - - + +
80B GLU* 1.3 57.7 + - - +
82B PHE* 3.2 8.5 + - + +
83B GLN* 2.9 30.1 + - - +
93B VAL* 3.7 33.4 - - + -
95B VAL* 4.2 8.7 - - + -
203B BCT 4.3 21.0 + - - +
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Residues in contact with GLU 80 (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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3A ALA* 3.7 24.0 - - - +
4A ILE* 4.6 13.1 + - + +
76B GLY 3.0 18.3 + - - +
77B PRO* 3.5 13.8 - - + +
78B LEU 3.2 0.2 - - - -
79B LEU* 1.3 77.0 - - - +
81B GLY* 1.3 61.7 + - - +
83B GLN* 3.2 14.6 + - - +
84B PRO* 3.1 21.0 - - - +
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Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B PHE* 4.3 10.7 - - - -
27B LEU* 3.5 27.3 - - - +
30B ARG* 5.8 0.9 - - - -
77B PRO 3.0 14.9 + - - -
78B LEU 3.1 4.0 + - - -
80B GLU* 1.3 76.1 - - - +
82B PHE* 1.3 60.6 + - - +
84B PRO* 3.4 11.9 - - - +
85B PHE 4.6 1.0 + - - -
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Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 5.6 2.2 - - + -
14B ILE* 3.9 37.9 - - + -
16B LEU* 4.6 4.0 - - + -
23B PHE* 4.4 10.5 - + - -
24B ALA* 3.9 40.2 - - + -
27B LEU* 3.6 24.0 - - + -
28B LEU* 4.3 11.9 - - + -
78B LEU* 2.9 31.1 + - + +
79B LEU* 3.9 10.1 - - + +
81B GLY* 1.3 76.3 - - - +
83B GLN* 1.3 65.7 + - - +
84B PRO 3.5 0.4 - - - -
85B PHE* 3.1 8.8 + + - +
86B PHE* 3.1 50.9 + + + -
93B VAL* 5.0 6.5 - - + -
203B BCT 5.1 1.8 - - - +
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Residues in contact with GLN 83 (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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4A ILE* 5.3 7.1 - - - +
79B LEU 2.9 12.0 + - - +
80B GLU* 3.2 19.5 + - - +
82B PHE* 1.3 79.1 - - - +
84B PRO* 1.3 72.8 - - + +
86B PHE* 3.4 1.7 + - - +
87B GLU* 3.2 23.2 + - + +
203B BCT 3.8 21.9 + - - +
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Residues in contact with PRO 84 (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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80B GLU 3.1 16.4 - - - +
81B GLY* 3.4 11.9 - - - +
83B GLN* 1.3 93.6 - - + +
85B PHE* 1.3 60.8 + - - +
87B GLU* 3.3 24.0 + - + +
88B ALA* 3.6 8.0 + - - +
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Residues in contact with PHE 85 (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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16B LEU* 3.9 18.6 - - + -
20B HIS* 3.6 45.5 - + + -
23B PHE* 3.6 44.8 - + + -
81B GLY 4.6 0.4 + - - -
82B PHE* 3.1 15.1 + + - +
84B PRO* 1.3 80.3 - - - +
86B PHE* 1.3 94.7 + + - +
88B ALA 3.2 3.1 + - - -
89B HIS* 2.8 64.9 + + + +
90B SER 4.2 3.8 - - - -
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Residues in contact with PHE 86 (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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102A ARG* 3.6 27.1 + - - +
14B ILE* 4.1 13.5 - - + -
15B ILE 3.8 9.9 - - - -
16B LEU* 4.4 1.6 - - + -
82B PHE* 3.1 42.8 + + + +
83B GLN 4.3 1.3 - - - +
85B PHE* 1.3 92.3 - + - +
87B GLU* 1.3 64.1 + - - +
88B ALA 3.2 1.1 - - - -
89B HIS 3.3 22.6 - - - +
90B SER 3.5 11.0 - - - -
91B GLY* 3.4 34.3 - - - -
92B VAL 4.1 1.3 - - - -
93B VAL* 3.4 27.8 - - + -
203B BCT 3.9 19.3 - - - +
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Residues in contact with GLU 87 (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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83B GLN* 3.2 16.7 + - + +
84B PRO* 3.5 17.9 - - - +
85B PHE 3.2 0.8 - - - -
86B PHE* 1.3 78.9 - - - +
88B ALA* 1.3 59.1 + - + +
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Residues in contact with ALA 88 (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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84B PRO 3.6 6.7 + - - +
85B PHE 3.2 3.0 + - - +
87B GLU* 1.3 82.1 - - + +
89B HIS* 1.3 81.6 + - + +
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Residues in contact with HIS 89 (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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102A ARG* 5.1 1.2 + - - -
17B GLU* 5.0 1.8 + - - -
20B HIS* 3.6 29.6 + + + -
85B PHE* 2.8 60.3 + + + +
86B PHE* 3.3 23.2 - - - +
87B GLU 3.7 0.4 - - - -
88B ALA* 1.3 94.6 + - + +
90B SER* 1.3 65.1 + - - +
91B GLY 4.0 0.5 + - - +
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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
------------------------------------------------------------
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