Contacts of the strand formed by residues 72 - 82 (chain L) in PDB entry 1N13
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 LEU 72 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14G LEU* 4.5 5.0 - - + +
15G PRO* 4.0 15.0 - - + -
51G ILE* 4.3 5.6 - - + -
74H PRO* 3.8 35.9 - - + -
162H LEU* 4.4 6.1 - - + -
164H TYR* 3.9 12.6 - - - +
6I ASN* 5.6 0.2 + - - -
8I LEU* 3.7 32.4 - - + +
9I HIS* 4.0 15.5 + - + +
47K ASN* 3.7 31.6 - - + +
49K ILE* 4.2 14.3 - - + +
70L GLY 4.2 1.8 - - - +
71L ALA* 1.3 69.8 - - - +
73L VAL* 1.3 59.7 + - - +
74L PRO* 3.4 12.1 - - - +
163L TRP* 3.7 11.4 - - - -
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Residues in contact with VAL 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K ILE* 6.4 0.4 - - + -
46K VAL* 4.1 18.2 - - + -
47K ASN 2.8 14.0 + - - +
48K LEU* 3.6 2.4 - - + -
49K ILE* 2.8 24.6 + - - -
67L LEU* 4.2 15.5 - - + -
71L ALA* 3.8 25.4 - - + +
72L LEU* 1.3 73.3 - - - +
74L PRO* 1.4 61.3 - - - +
75L THR* 2.9 25.0 + - - +
161L ALA* 3.9 17.5 - - + -
162L LEU 3.5 20.6 - - - +
163L TRP* 4.1 11.9 - - + -
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Residues in contact with PRO 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I ASN* 4.7 4.5 - - - +
8I LEU* 4.1 13.0 - - + -
72J LEU* 3.9 30.5 - - + -
15K PRO* 4.6 6.5 - - + -
49K ILE* 3.3 12.3 - - + +
51K ILE* 3.9 19.3 - - + -
72L LEU 3.4 8.3 - - - +
73L VAL* 1.4 80.0 - - - +
75L THR* 1.3 60.3 + - - +
162L LEU* 2.9 55.3 + - + +
163L TRP* 4.5 5.6 - - + -
164L TYR* 5.8 0.7 - - + -
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Residues in contact with THR 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K ILE* 5.0 0.4 - - + -
48K LEU* 3.4 26.9 - - + +
49K ILE 2.8 11.6 + - - -
50K ARG* 3.2 9.5 - - - +
51K ILE* 3.0 24.1 + - - +
73L VAL* 2.9 24.1 + - - +
74L PRO* 1.3 74.8 + - - +
76L ALA* 1.3 65.6 + - - +
77L TYR* 3.8 14.2 - - + -
159L ALA* 3.5 27.8 - - + -
160L ALA 3.5 13.9 - - - +
161L ALA* 4.1 5.1 - - + +
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Residues in contact with ALA 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K ILE* 3.5 28.3 - - + +
53L PYR 4.1 8.1 - - + -
75L THR* 1.3 70.6 - - - +
77L TYR* 1.3 60.5 + - - +
93L ILE* 3.7 3.5 - - + +
107L ILE* 3.8 28.5 - - + -
109L GLU* 4.4 10.8 - - - +
159L ALA* 3.2 3.5 - - - +
160L ALA* 2.8 35.5 + - + +
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Residues in contact with TYR 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G SER* 2.7 34.4 + - - -
34K PHE* 4.1 12.8 - + - -
48K LEU* 4.1 13.5 - - + -
50K ARG* 2.9 73.2 + - + +
75L THR* 3.8 20.9 - - + -
76L ALA* 1.3 75.6 - - - +
78L GLY* 1.3 60.1 + - - +
79L TYR* 3.8 22.0 - + - -
93L ILE* 4.4 2.5 - - - -
109L GLU* 3.7 16.9 + - - +
157L PHE* 3.6 15.7 - + + -
158L ALA 3.2 13.7 - - - +
159L ALA* 3.5 11.4 - - + +
7002L MRD 3.7 8.3 - - - +
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Residues in contact with GLY 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K ARG* 4.4 2.7 - - - -
77L TYR* 1.3 74.1 - - - +
79L TYR* 1.3 63.6 + - - +
91L ALA* 3.7 7.6 - - - +
92L ALA 5.3 0.7 - - - -
109L GLU* 3.9 14.6 - - - +
110L TYR 4.6 4.5 - - - -
111L GLU* 3.5 16.2 - - - -
157L PHE* 3.5 2.4 - - - -
158L ALA* 2.9 32.1 + - - +
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Residues in contact with TYR 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K PHE* 3.8 25.4 - + + -
50K ARG* 3.9 24.8 + - - +
77L TYR* 3.8 16.8 - + - -
78L GLY* 1.3 75.1 - - - +
80L ILE* 1.3 66.4 + - - +
81L ILE* 3.9 24.9 - - + -
91L ALA* 4.5 0.4 - - - -
111L GLU* 3.2 23.6 + - - +
155L CYS* 4.5 1.1 - - - -
156L ALA 3.2 13.2 - - - +
157L PHE* 4.1 7.2 - - + -
7002L MRD 3.1 43.9 + - + +
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Residues in contact with ILE 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L TYR* 1.3 79.3 - - - +
81L ILE* 1.3 74.8 + - - +
82L SER* 5.7 0.7 - - - -
89L ILE* 3.6 32.3 - - + +
90L SER 3.5 23.3 - - - +
111L GLU* 4.0 9.0 - - + -
112L GLY* 3.6 32.1 - - - +
113L LYS* 3.9 14.8 - - + +
155L CYS* 3.2 4.7 - - - -
156L ALA* 3.0 37.4 + - + +
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Residues in contact with ILE 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K PRO* 3.6 29.8 - - + +
34K PHE* 4.5 3.8 - - + -
79L TYR* 3.9 17.0 - - + -
80L ILE* 1.3 86.5 - - - +
82L SER* 1.3 66.2 + - - +
153L LEU* 3.8 23.3 - - + -
154L GLY 3.3 11.0 - - - +
155L CYS* 4.0 14.8 - - + -
7002L MRD 3.5 34.1 - - + +
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Residues in contact with SER 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80L ILE* 5.4 0.7 - - - -
81L ILE* 1.3 79.1 - - - +
83L ASP* 1.3 61.8 + - - +
84L VAL* 3.2 15.7 + - - +
87L GLU* 2.7 29.8 + - - -
89L ILE* 3.7 19.2 - - - +
113L LYS* 5.7 1.8 - - - -
150L VAL* 3.5 13.9 - - - +
153L LEU* 3.3 2.1 - - - +
154L GLY 2.9 32.1 + - - -
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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