Contacts of the strand formed by residues 38 - 44 (chain C) in PDB entry 1NVE
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 THR 38 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C SER* 2.8 20.9 + - - -
37C THR* 1.3 88.6 + - - +
39C TYR* 1.3 66.6 + - - +
40C VAL* 4.3 7.0 - - + -
71C ARG* 2.8 42.1 + - + +
73C LEU* 3.9 9.6 - - + -
103C CYS* 3.9 27.0 - - - -
104C GLY 5.3 0.5 + - - -
106C ASP* 4.7 3.5 + - - -
107C THR* 4.1 14.8 - - - +
108C VAL 3.0 17.9 + - - -
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Residues in contact with TYR 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C LEU* 3.2 42.9 + - + -
31C ILE* 3.2 21.0 - - + +
34C CYS 2.5 29.6 + - - -
36C SER* 3.3 31.2 + - - -
38C THR* 1.3 74.7 - - - +
40C VAL* 1.3 63.8 + - - +
55C PHE* 6.3 0.2 - - + -
59C PHE* 3.7 21.1 - + + -
70C PRO* 4.0 12.3 - - + -
71C ARG 3.0 12.8 + - - +
72C LEU* 3.4 18.5 - - + +
73C LEU* 2.8 26.9 + - - +
108C VAL* 3.3 27.6 - - + +
110C ILE* 4.4 3.8 - - + -
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C THR* 4.3 3.4 - - + -
39C TYR* 1.3 72.2 - - - +
41C LEU* 1.3 56.9 + - - +
42C VAL* 4.1 15.9 - - + -
73C LEU* 3.4 6.5 - - + -
95C TRP* 3.5 29.4 - - + -
96C MET* 4.1 17.5 - - + -
103C CYS* 3.8 22.9 - - - -
107C THR* 3.7 20.2 - - + -
108C VAL 3.0 8.3 + - - -
109C VAL* 3.2 17.3 - - + +
110C ILE* 2.6 32.7 + - - -
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Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C TRP* 4.4 4.3 - - + -
39C TYR 3.8 1.2 + - - -
40C VAL* 1.3 74.0 - - - +
42C VAL* 1.3 71.1 + - - +
43C THR* 4.8 1.8 - - + -
52C THR* 4.3 17.5 - - + +
55C PHE* 4.5 18.4 - - + -
72C LEU* 4.1 13.9 - - + -
73C LEU 2.7 14.5 + - - +
74C ILE* 3.5 22.4 - - + -
75C TYR* 2.8 28.6 + - - +
110C ILE* 3.5 23.8 - - + +
112C LEU* 3.4 44.6 - - + -
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Residues in contact with VAL 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 4.1 18.4 - - + -
41C LEU* 1.3 78.8 - - - +
43C THR* 1.3 67.5 + - - +
75C TYR* 3.5 15.5 - - + +
77C ARG* 5.5 0.7 - - + -
92C ILE* 4.0 34.5 - - + -
109C VAL* 4.1 4.5 - - + -
110C ILE 3.0 4.9 + - - -
112C LEU* 3.0 27.2 + - - +
117C ILE* 3.6 13.4 - - + +
120C LEU* 4.8 1.6 - - + -
121C THR* 3.4 37.5 - - + +
124C VAL* 6.2 0.7 - - + -
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 4.8 6.7 - - + -
42C VAL* 1.3 76.1 - - - +
44C ASP* 1.3 70.3 + - - +
47C ILE* 3.3 20.8 - - - +
48C GLY* 3.9 12.1 - - - -
52C THR* 4.2 6.1 - - - +
74C ILE* 5.1 0.9 - - + -
75C TYR 3.2 6.9 + - - +
76C ASN* 3.4 22.5 - - - +
77C ARG* 2.9 23.9 + - - +
112C LEU* 2.4 38.7 + - + -
117C ILE* 3.7 15.0 - - - +
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Residues in contact with ASP 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C THR* 1.3 80.7 + - - +
45C THR* 1.3 57.2 + - - +
46C ASN 3.1 4.2 + - - -
47C ILE* 2.9 31.3 + - - +
48C GLY* 2.8 25.3 + - - -
76C ASN* 4.5 3.4 - - - -
77C ARG 2.9 17.7 - - - +
78C PRO 4.0 2.0 - - - +
79C PRO* 3.2 26.1 - - + +
80C GLY 4.5 0.9 + - - -
117C ILE* 4.0 12.4 - - + +
402C NAD 2.6 26.3 + - - +
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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