Contacts of the strand formed by residues 16 - 21 (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 PRO 16 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LYS 4.7 1.1 - - - +
15G SER* 1.3 92.2 + - - +
17G VAL* 1.3 64.6 + - - +
29G GLY 3.4 11.2 - - - +
30G THR* 4.4 4.5 - - - +
72G PRO* 3.9 3.1 - - - +
73G ALA* 3.5 37.9 + - + +
74G PRO 4.9 5.2 - - - +
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Residues in contact with VAL 17 (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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12G SER* 4.5 13.0 - - - -
15G SER* 4.0 8.3 - - - +
16G PRO* 1.3 80.2 - - - +
18G ILE* 1.3 64.3 + - - +
19G VAL* 4.0 13.0 - - + -
27G PHE 3.6 1.2 - - - +
28G ARG* 3.4 6.6 - - - +
29G GLY 2.8 38.4 + - - +
31G LEU* 4.1 26.2 - - + -
42G LEU* 3.9 21.8 - - + -
70G VAL* 4.2 13.2 - - + -
71G SER 3.4 12.3 - - - +
72G PRO* 4.6 5.4 - - + -
73G ALA* 4.7 2.7 - - - +
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Residues in contact with ILE 18 (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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55A ARG* 3.1 36.8 - - - +
17G VAL* 1.3 75.8 - - - +
19G VAL* 1.3 64.8 + - - +
20G ARG 4.0 0.2 + - - -
26G GLU* 3.6 20.4 - - + +
27G PHE 3.5 5.6 - - - +
28G ARG* 4.0 21.3 - - + +
69G PHE* 3.6 7.7 - - + +
70G VAL* 3.3 5.0 - - - -
71G SER* 2.7 51.3 + - - +
72G PRO 5.0 0.7 - - - +
73G ALA* 4.0 25.1 - - + -
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Residues in contact with VAL 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G VAL* 4.0 20.0 - - + -
18G ILE* 1.3 77.6 - - - +
20G ARG* 1.3 60.2 + - - +
21G LEU* 3.7 22.1 + - + +
26G GLU* 3.5 6.1 - - - -
27G PHE* 2.9 42.0 + - + +
40G LEU* 3.8 33.0 - - + -
42G LEU* 4.4 12.8 - - + -
62G ILE* 4.1 10.1 - - + -
67G VAL* 4.3 8.1 - - + -
69G PHE 3.5 5.8 - - - +
70G VAL* 4.1 6.1 - - + -
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Residues in contact with ARG 20 (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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25A ARG* 2.6 38.5 - - - +
47A GLU* 3.2 17.5 + - - -
55A ARG* 4.6 3.8 - - - +
18G ILE* 4.0 1.4 + - - +
19G VAL* 1.3 71.4 - - - +
21G LEU* 1.3 65.2 + - - +
24G GLY* 2.9 36.5 + - - -
25G ARG 4.0 4.5 + - - -
26G GLU* 4.0 22.9 + - + -
67G VAL* 3.7 3.1 - - - -
68G VAL* 2.7 46.6 + - + -
69G PHE* 2.8 49.5 + - + +
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Residues in contact with LEU 21 (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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20F ARG* 6.1 2.2 - - - +
68F VAL* 3.8 16.8 - - + -
69F PHE* 5.2 0.9 - - + -
19G VAL* 4.0 22.7 - - + +
20G ARG* 1.3 88.4 - - - +
22G LYS* 1.3 67.5 + - - +
23G GLY 3.6 1.6 + - - -
24G GLY 3.8 8.4 + - - -
25G ARG* 3.2 29.6 + - + +
27G PHE* 4.2 25.4 - - + -
62G ILE* 4.0 14.4 - - + -
66G THR* 3.3 38.8 - - + +
67G VAL* 4.2 1.1 - - - -
68G VAL* 3.4 10.1 - - - +
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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