Contacts of the strand formed by residues 67 - 72 (chain G) in PDB entry 1I5L
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 VAL 67 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL 5.6 0.2 - - - +
63A ARG* 3.5 28.1 + - + +
66A THR* 4.3 0.3 + - - -
19G VAL* 4.3 6.3 - - + -
20G ARG 3.7 5.2 - - - +
21G LEU* 4.2 1.3 - - - -
22G LYS* 3.5 13.6 + - - -
38G MET* 4.4 7.9 - - + +
40G LEU* 4.2 16.6 - - + -
62G ILE* 4.0 16.6 - - + -
63G ARG 4.0 9.6 - - - +
64G GLY* 3.0 21.2 + - - +
66G THR* 1.3 76.1 - - - +
68G VAL* 1.3 63.5 + - - +
69G PHE* 3.5 17.0 - - - +
70G VAL* 3.9 22.9 - - + -
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Residues in contact with VAL 68 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 4.4 11.9 - - + -
62A ILE* 4.0 4.6 - - + +
63A ARG* 3.2 22.9 + - - +
66A THR* 3.9 27.9 - - + +
20G ARG* 2.7 20.5 + - + +
21G LEU 3.4 28.5 - - - +
22G LYS* 3.6 20.4 - - + -
67G VAL* 1.3 74.7 - - - +
69G PHE* 1.3 78.8 + - + +
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Residues in contact with PHE 69 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A PHE* 3.6 35.0 - + - -
47A GLU* 4.3 10.3 - - - -
55A ARG* 3.8 34.5 - - - -
57A VAL* 5.7 1.3 - - + -
60A VAL* 4.0 20.0 - - + -
61A VAL 3.4 14.1 - - - +
62A ILE* 4.3 11.2 - - + -
18G ILE* 4.6 6.3 - - + -
19G VAL* 3.5 2.6 - - - -
20G ARG* 2.8 60.5 + - + +
67G VAL* 3.5 4.7 - - - +
68G VAL* 1.3 93.9 - - + +
70G VAL* 1.3 71.2 + - - +
71G SER* 4.4 8.5 - - - -
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Residues in contact with VAL 70 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 3.7 0.3 - - - -
61A VAL* 3.0 38.9 + - + +
9G LEU* 4.1 26.9 - - + -
17G VAL* 4.2 19.1 - - + -
18G ILE 3.3 7.2 - - - +
19G VAL* 4.1 12.3 - - + -
31G LEU* 5.5 1.6 - - + -
38G MET* 5.7 4.5 - - + -
40G LEU* 3.8 28.3 - - + -
67G VAL* 3.9 12.1 - - + -
69G PHE* 1.3 82.1 - - - +
71G SER* 1.3 67.3 + - - +
72G PRO* 4.6 0.3 - - - +
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Residues in contact with SER 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A VAL* 3.9 15.6 - - - +
59A SER 3.2 18.9 + - - -
60A VAL* 3.4 16.6 - - - -
17G VAL* 3.4 6.3 - - - +
18G ILE* 2.7 47.8 + - - +
69G PHE* 4.3 8.7 - - - -
70G VAL* 1.3 76.9 - - - +
72G PRO* 1.4 76.3 + - - +
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Residues in contact with PRO 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A VAL* 5.5 1.4 - - - +
58A GLY 5.4 4.7 + - - -
59A SER* 3.3 33.4 - - - +
8G VAL* 5.8 6.1 - - + -
12G SER* 4.7 15.7 - - - +
15G SER* 6.0 1.1 - - - +
16G PRO 3.9 9.0 - - - +
17G VAL* 4.6 3.4 - - + -
18G ILE* 5.0 2.0 - - - +
70G VAL 4.6 0.7 - - - +
71G SER* 1.4 97.3 + - - +
73G ALA* 1.3 61.5 + - - +
74G PRO* 4.0 8.0 - - + +
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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