Contacts of the strand formed by residues 97 - 106 (chain B) in PDB entry 1D7I
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 LEU 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B MET 3.7 2.9 - - - +
30B LEU* 3.7 21.5 - - + -
36B PHE* 3.7 26.5 - - + -
56B ILE* 4.7 0.4 - - + -
74B LEU 3.8 0.3 - - - +
75B THR* 3.5 2.9 - - - -
76B ILE* 2.8 43.6 + - + +
81B ALA* 3.9 12.1 - - + -
82B TYR* 3.7 36.1 - - + -
91B ILE* 4.1 11.4 - - + -
95B ALA* 3.7 10.3 + - + +
96B THR* 1.3 79.3 - - - +
98B VAL* 1.3 63.5 - - - +
99B PHE* 3.6 29.6 - - + -
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Residues in contact with VAL 98 (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 THR 3.8 0.9 - - - +
28B GLY* 3.6 1.0 - - - -
29B MET* 2.8 60.9 + - + +
30B LEU 5.1 0.7 - - - +
31B GLU* 5.1 15.0 - - - -
73B LYS* 3.8 32.1 - - + -
74B LEU 3.3 4.0 - - - +
75B THR* 4.1 18.4 - - + +
96B THR* 5.1 3.6 - - + +
97B LEU* 1.3 77.7 - - - +
99B PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 99 (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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26B TYR* 4.3 8.3 - + + -
27B THR 3.3 6.5 - - - -
28B GLY* 3.6 24.0 - - - -
36B PHE* 3.8 20.4 - + - -
56B ILE* 4.0 8.7 - - + -
59B TRP* 3.6 33.7 - + - +
72B ALA 3.5 1.2 - - - +
73B LYS* 3.3 4.9 - - - +
74B LEU* 2.7 45.4 + - + +
76B ILE* 3.8 13.9 - - + -
97B LEU* 3.6 30.1 - - + -
98B VAL* 1.3 80.6 - - - +
100B ASP* 1.3 59.5 + - - +
101B VAL* 3.6 16.1 + - + -
302B DSS 3.6 27.8 - - + -
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Residues in contact with ASP 100 (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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7B ILE* 3.7 19.9 - - + +
25B HIS 3.9 0.5 - - - +
26B TYR* 3.2 5.5 - - - -
27B THR* 3.0 37.3 + - - +
29B MET* 4.3 17.1 - - + +
40B ARG* 4.4 5.4 + - - -
71B ARG* 3.0 44.4 + - - +
72B ALA 3.6 3.8 - - - -
73B LYS* 4.6 4.9 - - + +
99B PHE* 1.3 69.9 - - - +
101B VAL* 1.3 62.0 + - - +
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Residues in contact with VAL 101 (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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24B VAL* 4.0 25.1 - - + -
25B HIS 3.5 8.3 - - - +
26B TYR* 4.2 9.9 - - + -
59B TRP* 4.4 10.5 - - + -
63B VAL* 4.4 14.1 - - + -
66B MET* 3.4 16.3 - - - +
71B ARG* 3.3 1.1 - - - -
72B ALA 2.8 38.3 + - - +
74B LEU* 4.1 16.4 - - + -
99B PHE* 3.8 22.9 - - + -
100B ASP* 1.3 80.2 - - - +
102B GLU* 1.3 65.6 + - - +
103B LEU* 4.6 0.7 - - + +
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Residues in contact with GLU 102 (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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24B VAL* 3.3 6.9 - - - -
25B HIS* 3.0 30.0 + - + +
40B ARG* 3.2 32.7 + - - +
69B GLY* 4.5 8.1 - - - +
70B GLN 3.4 12.1 - - - +
71B ARG* 3.7 28.0 + - + +
101B VAL* 1.3 76.1 - - - +
103B LEU* 1.3 62.3 + - - +
104B LEU* 3.4 27.3 + - + +
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Residues in contact with LEU 103 (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 PRO* 3.9 24.7 - - + -
22B CYS* 4.1 8.5 - - + -
23B VAL 3.9 7.4 - - - +
24B VAL* 4.0 16.2 - - + -
63B VAL* 4.6 5.8 - - + +
66B MET* 4.1 20.4 - - + +
67B SER 3.7 27.8 - - - +
68B VAL* 3.7 8.7 - - + +
69B GLY* 2.8 34.7 + - - -
70B GLN 2.8 15.0 + - - +
101B VAL* 4.2 1.0 - - + -
102B GLU* 1.3 69.5 - - - +
104B LEU* 1.3 56.8 + - - +
105B LYS 3.7 20.0 - - - +
106B LEU* 3.9 15.0 - - + -
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Residues in contact with LEU 104 (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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23B VAL* 2.8 21.2 + - + +
24B VAL* 4.7 2.2 - - - -
25B HIS* 4.3 18.6 - - + +
45B PRO* 3.9 34.1 - - + -
68B VAL* 3.9 9.1 - - - +
69B GLY* 4.9 2.1 + - - -
102B GLU* 3.5 35.4 - - + +
103B LEU* 1.3 73.6 - - - +
105B LYS* 1.3 71.0 + - + +
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Residues in contact with LYS 105 (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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23B VAL* 3.1 44.0 + - + -
68B VAL* 4.0 12.5 - - + +
103B LEU* 3.6 4.3 - - - +
104B LEU* 1.3 83.1 - - + +
106B LEU* 1.3 73.7 + - - +
107B GLU* 3.0 38.5 + - - +
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Residues in contact with LEU 106 (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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14B THR* 4.1 22.2 - - + -
15B PHE 4.2 1.1 - - - +
16B PRO* 3.8 36.6 - - + -
20B GLN* 3.7 38.4 - - + +
21B THR 3.3 3.8 - - - +
22B CYS* 4.0 15.7 - - - -
68B VAL* 3.8 13.6 - - + +
103B LEU* 3.9 15.5 - - + -
105B LYS* 1.3 88.0 - - - +
107B GLU* 1.3 63.8 + - - +
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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