Contacts of the strand formed by residues 46 - 54 (chain A) in PDB entry 3KVF
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 ALA 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 4.6 3.6 - - + -
43A PRO 4.0 4.9 - - - +
44A ALA* 4.0 2.0 - - - +
45A PRO* 1.3 74.0 - - - +
47A CYS* 1.3 59.8 + - - +
48A ALA 3.6 2.0 - - - +
190A GLU* 4.2 11.1 + - - +
193A LEU* 3.3 21.0 - - - +
194A LEU* 3.7 39.1 - - + +
218A ALA* 4.8 3.1 - - + -
219A LEU 3.6 7.4 - - - +
220A CYS* 3.8 14.8 - - + -
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TRP* 3.6 28.3 - - + -
46A ALA* 1.3 73.9 - - - +
48A ALA* 1.3 62.1 + - - +
102A ASN* 3.5 35.7 + - - +
105A LYS* 4.5 8.5 - - + +
106A LEU* 4.4 5.8 - - - -
166A ASN* 3.9 8.7 - - - +
167A ASN 4.4 0.3 + - - -
190A GLU* 4.8 4.6 - - - +
193A LEU* 3.2 20.9 - - - +
219A LEU* 2.9 45.6 + - - -
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Residues in contact with ALA 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 5.4 1.0 - - + -
46A ALA* 3.6 1.5 - - - +
47A CYS* 1.3 83.1 - - - +
49A LEU* 1.3 59.5 + - - +
50A LEU* 5.7 0.2 - - - -
98A ALA* 4.2 4.3 - - + -
102A ASN* 4.3 6.7 - - - +
164A LEU* 3.6 23.8 - - + -
165A PHE 3.6 6.3 - - - +
166A ASN* 4.4 2.5 - - - +
193A LEU* 5.1 1.3 - - - +
194A LEU* 5.5 3.6 - - - -
217A VAL 4.2 0.2 - - - +
218A ALA* 3.5 4.0 - - - +
219A LEU* 2.8 54.9 + - + +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 4.1 24.5 - - + -
34A LEU* 5.3 5.4 - - + -
39A LEU* 5.8 4.7 - - + -
48A ALA* 1.3 74.4 - - - +
50A LEU* 1.3 65.4 + - - +
164A LEU* 3.4 4.9 - - - +
165A PHE* 2.7 45.1 + - + +
193A LEU* 5.9 2.7 - - + +
194A LEU* 4.5 19.3 - - + +
197A ALA* 3.7 31.2 - - + -
198A ALA* 4.3 9.2 - - + +
201A CYS* 3.9 23.1 - - - -
216A ALA* 4.6 7.0 - - + -
217A VAL 3.7 16.2 - - - +
218A ALA* 4.2 6.5 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 4.7 1.4 - - - +
13A LEU* 3.8 23.1 - - + -
28A PHE* 4.4 13.9 - - + -
49A LEU* 1.3 76.1 - - - +
51A LEU* 1.3 59.8 + - - +
91A GLY 5.4 0.2 - - - +
94A GLY* 4.1 20.9 - - - -
95A LEU* 4.5 8.3 - - + -
98A ALA* 5.4 0.2 - - + -
162A PHE* 3.5 37.2 - - + -
163A ILE 3.5 5.6 - - - +
164A LEU* 3.5 34.3 - - + -
216A ALA* 3.3 8.0 - - - +
217A VAL* 2.9 43.5 + - + +
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Residues in contact with LEU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A LEU* 5.7 2.2 - - + -
49A LEU* 4.2 0.6 - - + -
50A LEU* 1.3 74.4 - - - +
52A LEU* 1.3 70.5 + - - +
53A PHE* 4.2 3.6 - - + -
161A HIS 3.3 2.1 - - - +
162A PHE* 3.3 5.4 - - - -
163A ILE* 2.8 67.5 + - + +
165A PHE* 4.0 9.6 - - + -
201A CYS* 3.7 33.9 - - + +
204A PHE* 4.1 26.7 - - + -
214A PHE* 4.7 9.4 - - + -
215A SER 3.4 18.6 - - - +
216A ALA* 4.6 6.7 - - + -
8B LEU* 4.7 8.5 - - + -
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ILE* 3.6 19.7 - - + +
51A LEU* 1.3 74.7 - - - +
53A PHE* 1.3 62.7 + - - +
160A PHE* 3.7 34.8 - - + -
161A HIS 3.2 7.0 - - - +
162A PHE* 3.6 30.1 - - + -
213A ARG 4.6 0.2 - - - +
214A PHE* 3.4 5.0 - - - +
215A SER* 2.8 40.4 + - - +
73B LEU* 3.4 45.8 - - + +
75B GLY* 3.9 11.0 - - - +
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A LEU* 4.3 5.6 - - + -
52A LEU* 1.3 75.6 - - - +
54A PRO* 1.3 87.1 - - + +
55A LEU* 3.2 6.5 + - + -
59A HIS* 3.4 50.9 - + + -
63A ARG* 4.6 0.4 - - - -
160A PHE* 3.5 7.7 - - - -
161A HIS* 3.0 64.8 + + + -
163A ILE* 3.7 33.2 - - + -
204A PHE* 4.2 15.5 - + + -
208A GLU* 6.2 1.8 - - + -
214A PHE* 3.5 18.8 - + + -
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Residues in contact with PRO 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A PHE* 1.3 96.4 - - + +
55A LEU* 1.3 61.4 + - - +
56A THR* 2.8 29.9 + - + +
59A HIS* 4.6 1.7 - - - +
159A ASN 4.6 0.9 - - - +
160A PHE* 3.4 19.3 - - + -
208A GLU* 4.5 5.7 - - + +
211A GLU* 3.5 33.7 - - + +
213A ARG 3.2 18.4 - - - +
214A PHE* 3.5 16.8 - - + -
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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