Contacts of the strand formed by residues 72 - 77 (chain K) in PDB entry 3GTL
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 72 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551A TYR* 4.1 12.7 + - - +
32K VAL* 4.0 25.6 - - + -
33K ILE 3.5 4.3 - - - +
34K THR* 4.0 20.0 - - + +
60K ALA 3.5 1.0 - - - +
61K TYR* 2.9 27.1 - - - +
62K LYS* 3.1 20.3 + - + +
64K GLU* 3.4 37.8 + - + +
70K ARG* 5.4 8.3 - - - +
71K PHE* 1.3 81.5 - - - +
73K LEU* 1.3 59.7 + - - +
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Residues in contact with LEU 73 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31K VAL 3.7 0.9 - - - +
32K VAL* 3.2 3.6 - - - -
33K ILE* 2.8 43.6 + - + +
35K PHE* 3.7 24.6 - - + -
43K GLY 5.2 0.7 - - - +
46K ILE* 3.5 29.4 - - + -
47K ARG* 4.0 20.6 - - + +
50K LEU* 4.0 2.0 - - + -
59K ALA 5.3 0.2 - - - -
60K ALA 3.2 18.8 - - - +
61K TYR* 3.6 17.9 - - + -
71K PHE* 4.4 5.4 + - + -
72K LYS* 1.3 72.6 - - - +
74K ARG* 1.3 59.7 + - - +
75K ILE* 3.6 28.9 + - + -
87K LEU* 4.1 7.0 - - + -
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Residues in contact with ARG 74 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A TYR* 3.6 37.8 - - + +
556A TRP* 3.8 23.0 - - - -
558A GLY* 4.1 5.8 - - - -
24K ASP* 2.9 46.2 + - - +
26K LYS* 5.0 1.6 - - - +
27K ALA* 3.9 10.9 - - - +
30K ALA* 3.5 13.3 - - - +
31K VAL 3.0 20.0 - - - +
32K VAL* 4.3 3.4 - - + -
58K PHE* 3.1 42.1 - - + -
59K ALA* 3.4 1.0 - - - -
60K ALA 2.8 33.2 + - - -
73K LEU* 1.3 73.4 - - - +
75K ILE* 1.3 61.6 + - - +
76K GLN* 4.0 18.8 - - - +
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Residues in contact with ILE 75 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K ASN 4.1 1.6 - - - +
30K ALA* 3.5 3.0 - - - -
31K VAL* 2.8 34.8 + - + +
33K ILE* 4.1 19.7 - - + -
50K LEU* 3.4 46.7 - - + -
56K VAL* 3.8 8.1 - - + -
58K PHE* 3.2 12.3 - - - +
59K ALA* 4.8 2.2 - - - -
73K LEU* 3.6 22.2 - - + -
74K ARG* 1.3 79.6 - - - +
76K GLN* 1.3 63.1 + - - +
77K THR* 4.3 9.4 - - + -
83K PRO* 4.4 15.9 - - + +
86K ALA* 4.7 4.5 - - + -
87K LEU* 4.2 11.0 - - + -
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Residues in contact with GLN 76 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A TRP* 6.1 0.2 - - - -
558A GLY 4.5 5.3 + - - -
560A ILE* 5.9 1.8 - - - +
78H SER* 4.3 15.9 + - - -
27K ALA* 3.3 20.8 - - - +
28K PRO* 3.0 33.3 - - - +
29K ASN 3.9 2.7 - - - +
30K ALA* 4.0 9.6 - - + -
56K VAL* 3.3 7.4 - - - +
57K LEU* 2.8 43.6 + - + +
58K PHE* 2.9 30.7 + - + +
74K ARG* 4.0 14.8 - - - +
75K ILE* 1.3 74.4 - - - +
77K THR* 1.3 67.6 + - - +
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Residues in contact with THR 77 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29K ASN* 2.7 37.8 + - - +
55K LYS 3.7 15.7 - - - +
56K VAL* 3.8 10.3 - - + -
57K LEU* 3.6 16.6 - - - +
75K ILE* 4.3 4.5 - - + -
76K GLN* 1.3 82.0 - - - +
78K THR* 1.3 65.0 + - - +
79K GLU 3.7 0.3 + - - -
81K TYR* 3.0 23.8 + - + -
83K PRO* 3.4 12.5 - - + +
86K ALA* 3.7 29.6 - - + -
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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