Contacts of the strand formed by residues 74 - 80 (chain G) in PDB entry 5LN3
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 74 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69G ASN* 3.6 2.8 - - - +
70G VAL* 2.8 53.0 + - + +
73G HIS* 1.4 115.3 - - + +
75G GLY* 1.3 69.9 + - - +
107G ILE* 5.1 0.4 - - + -
108G PRO 6.4 0.2 - - - -
109G LEU* 4.1 22.7 - - + -
112G LEU* 4.1 21.3 - - + -
138G LEU* 4.6 6.1 - - + -
139G GLY 4.3 3.1 - - - +
140G SER* 4.4 1.6 - - - -
225G HIS* 3.7 11.5 - - - +
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Residues in contact with GLY 75 (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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48G PHE* 3.9 14.0 - - - -
68G PHE 4.2 0.4 - - - -
73G HIS 4.3 0.4 + - - -
74G VAL* 1.3 75.4 - - - +
76G MET* 1.4 61.2 + - - +
138G LEU* 3.3 26.2 - - - +
139G GLY 3.3 16.4 + - - -
140G SER* 4.7 0.4 - - - -
217G VAL* 5.2 1.9 - - - +
225G HIS* 3.6 24.8 - - - +
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Residues in contact with MET 76 (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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48G PHE* 4.5 2.5 - - - -
67G LEU* 3.6 5.4 - - - +
68G PHE* 2.6 58.4 + - + +
70G VAL* 3.6 31.0 - - + -
75G GLY* 1.4 70.3 - - - +
77G ALA* 1.4 60.4 + - - +
88G LEU* 4.9 10.1 - - + -
89G ALA* 4.5 15.7 - - - -
92G ALA* 5.1 8.5 - - + -
112G LEU* 5.6 2.9 - - + -
116G VAL* 5.5 5.2 - - + -
136G PHE* 3.9 30.7 - - + -
137G MET 3.5 3.6 - - - +
138G LEU* 3.9 44.6 - - + -
152G ILE* 5.9 0.7 - - + -
225G HIS* 4.9 2.1 + - - -
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Residues in contact with ALA 77 (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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37G ALA* 5.4 6.3 - - + -
38G ILE 6.0 0.4 - - - +
48G PHE* 4.6 13.0 - - + -
49G GLY 6.1 0.9 - - - +
50G VAL* 5.8 3.1 - - + -
66G ARG 3.7 8.1 - - - +
67G LEU* 4.0 21.1 - - + -
68G PHE* 5.5 0.4 - - - -
76G MET* 1.4 75.6 - - - +
78G VAL* 1.4 62.7 + - - +
136G PHE* 3.6 2.9 - - - +
137G MET* 2.8 51.5 + - + +
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Residues in contact with VAL 78 (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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37G ALA* 4.9 8.7 - - - +
50G VAL* 5.1 3.1 - - - +
66G ARG* 3.7 30.9 + - + +
68G PHE* 4.4 14.6 - - + -
77G ALA* 1.4 74.7 - - - +
79G ALA* 1.3 72.2 + - - +
80G GLY 6.1 0.7 - - - -
81G LEU 5.7 0.7 - - - +
82G LEU* 5.8 3.6 - - + -
85G ALA* 3.7 21.3 - - + -
134G CYS* 3.9 9.4 - - + -
135G SER 3.0 22.2 - - - +
136G PHE* 3.6 30.5 - - + -
137G MET* 4.9 0.4 - - - +
166G ILE* 4.7 4.5 - - - -
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Residues in contact with ALA 79 (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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31G VAL* 4.0 17.3 - - + +
34G SER* 4.8 5.4 - - - -
35G SER 5.6 2.7 - - - +
36G THR* 6.5 0.2 - - - -
37G ALA* 5.6 2.7 - - + +
66G ARG* 5.9 3.1 - - - +
78G VAL* 1.3 79.7 - - - +
80G GLY* 1.3 58.5 + - - +
134G CYS* 3.4 2.8 - - - -
135G SER* 2.9 32.1 + - - +
166G ILE* 3.4 34.1 - - + +
167G GLY* 5.2 3.6 - - - +
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Residues in contact with GLY 80 (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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30G ALA 5.0 1.1 - - - -
31G VAL* 4.3 4.9 - - - -
34G SER* 3.5 27.9 + - - -
66G ARG* 5.5 4.6 + - - +
78G VAL* 6.1 0.9 - - - -
79G ALA* 1.3 74.8 - - - +
81G LEU* 1.4 63.9 + - - -
82G LEU* 3.7 1.9 + - - -
133G GLY 3.5 14.8 - - - -
134G CYS* 4.4 0.9 - - - -
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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