Contacts of the strand formed by residues 60 - 65 (chain B) in PDB entry 1LI5
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 LYS 60 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A VAL* 5.2 14.8 - - - +
87A ALA* 6.2 0.6 - - - +
90A ASP* 3.1 27.1 + - - -
21B GLY 2.8 18.1 + - - +
22B GLU* 3.2 31.0 + - + +
23B VAL 2.9 23.3 + - - +
58B GLY 3.6 2.3 + - - +
59B TYR* 1.3 71.0 - - - +
61B LEU* 1.3 59.4 + - - +
62B LYS 4.2 0.2 + - - -
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B VAL* 3.5 34.8 - - + +
25B MET* 4.0 14.1 - - + -
51B ALA* 3.6 43.7 - - + +
54B LEU* 4.5 9.4 - - + -
55B ARG* 2.8 53.0 + - + +
59B TYR* 3.2 7.7 + - + +
60B LYS* 1.3 74.7 - - - +
62B LYS* 1.3 79.0 + - - +
63B TYR* 4.1 5.6 - - + +
109B ASP* 3.3 2.9 - - - +
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Residues in contact with LYS 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A SER* 4.2 24.0 + - - +
86A VAL* 5.8 6.3 - - + -
23B VAL 3.0 12.6 + - - +
24B GLY* 3.7 1.8 - - - -
25B MET 3.0 26.7 + - - +
60B LYS 4.2 0.2 + - - -
61B LEU* 1.3 73.7 - - - +
63B TYR* 1.3 59.4 - - - +
64B VAL* 3.9 4.7 + - + -
109B ASP* 3.4 11.4 - - + -
110B MET* 4.3 13.0 - - - +
216B GLN* 2.8 52.4 + - - +
217B LEU* 3.9 13.8 - - + +
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET* 3.7 22.7 - - + -
27B VAL* 3.6 33.8 - - + +
44B PHE* 4.6 4.3 + - - -
47B PHE* 3.9 17.9 - - - +
48B ASP* 5.0 4.6 + - - -
51B ALA* 4.2 18.8 - - + -
55B ARG* 4.7 3.4 - - - +
61B LEU* 4.1 17.0 - - + -
62B LYS* 1.3 70.6 - - - +
64B VAL* 1.3 71.0 + - - +
65B ARG* 3.4 28.3 + - + -
105B ILE* 6.3 1.6 - - + -
106B LEU* 4.7 9.9 - - + -
107B ARG 4.8 2.7 - - - -
108B PRO* 3.4 28.2 - - + +
109B ASP* 2.6 46.5 + - - +
110B MET 3.4 2.9 + - - -
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B MET 2.8 12.1 + - - +
26B TYR* 3.0 29.5 - - + -
27B VAL 3.0 23.0 + - - -
62B LYS* 4.4 6.5 - - + -
63B TYR* 1.3 77.8 - - - +
65B ARG* 1.3 63.6 + - - +
110B MET* 3.4 10.5 - - + +
112B PRO* 3.6 28.9 - - + -
212B MET 5.4 1.3 - - - +
216B GLN* 4.0 24.7 - - + -
217B LEU* 3.6 31.0 - - + -
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Residues in contact with ARG 65 (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 VAL* 3.2 17.0 - - - +
29B GLY* 4.1 8.3 - - - -
30B ILE 5.6 0.4 - - - +
44B PHE* 3.5 29.3 - - - +
63B TYR* 3.4 25.7 + - + -
64B VAL* 1.3 74.8 - - - +
66B ASN* 1.3 71.1 + - - +
67B ILE* 4.7 0.2 - - - +
96B MET* 4.4 5.7 - - - +
97B HIS* 5.1 3.2 + - - -
100B PHE* 3.9 31.4 - - - -
105B ILE* 5.5 4.2 - - - +
106B LEU 4.8 5.1 + - - -
107B ARG* 5.2 1.2 - - - +
108B PRO* 3.3 44.3 - - + +
110B MET 3.2 6.4 + - - -
111B GLU* 3.0 54.1 + - - +
112B PRO* 4.2 1.8 - - - -
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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