Contacts of the strand formed by residues 55 - 68 (chain D) in PDB entry 1NVP
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 ARG 55 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369C LYS* 3.4 33.1 - - + +
371C ILE* 3.5 27.8 - - + +
54D ASN* 1.3 75.2 - - - +
56D VAL* 1.3 78.6 + - - +
57D ASN* 3.7 24.7 + - - +
82D ARG 4.5 0.2 - - - +
83D GLU* 4.1 17.3 - - - +
84D VAL* 5.0 4.5 + - - +
16F C 5.6 3.8 - - - -
17F C 4.3 23.2 + - - -
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358C MET* 4.0 24.2 - - + -
366C ILE 4.6 1.3 - - - +
367C PHE* 3.4 26.0 - - + -
369C LYS 2.8 10.2 + - - +
370C ALA* 3.3 10.3 - - + -
371C ILE 3.0 18.2 + - - -
54D ASN* 4.5 1.6 - - - +
55D ARG* 1.3 81.7 - - - +
57D ASN* 1.3 96.3 + - - +
58D PHE* 5.4 0.4 - - + -
81D PHE* 4.5 11.0 - - + -
82D ARG 3.5 14.8 - - - +
83D GLU* 4.2 22.4 - - + +
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Residues in contact with ASN 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C ILE* 3.1 26.4 - - - +
55D ARG* 3.7 26.6 + - - +
56D VAL* 1.3 88.1 - - - +
58D PHE* 1.3 60.6 + - - +
81D PHE* 3.3 2.4 - - - -
82D ARG* 2.4 64.7 + - + +
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Residues in contact with PHE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351C PHE* 3.9 30.1 - + + -
353C LEU* 3.9 22.7 - - + -
370C ALA* 4.4 9.4 - - + -
371C ILE 2.9 19.2 + - - -
372C GLY* 2.8 56.0 - - - -
373C ASP* 2.8 5.0 + - - +
56D VAL* 5.4 0.7 - - + -
57D ASN* 1.3 77.5 - - - +
59D ARG* 1.3 64.9 + - - +
76D LEU* 4.6 10.1 - - + -
79D VAL* 4.0 16.2 - - + -
80D GLU 3.2 8.7 - - - +
81D PHE* 3.6 32.3 - + + -
95D ILE* 3.8 21.8 - - + -
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Residues in contact with ARG 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C ASP* 3.2 40.9 + - + +
58D PHE* 1.3 76.2 - - - +
60D GLY* 1.3 63.7 + - - +
78D ASP 3.9 0.9 - - - +
79D VAL* 3.2 6.5 - - - -
80D GLU* 2.9 37.2 + - + +
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Residues in contact with GLY 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C ASP 2.9 6.3 + - - +
374C ALA* 2.9 27.1 - - - +
375C GLU 3.5 1.9 + - - -
59D ARG* 1.3 81.3 - - - +
61D SER* 1.3 61.6 + - - -
76D LEU* 4.2 6.4 - - - +
77D ASN 3.8 2.5 - - - -
78D ASP 3.7 15.0 - - - -
79D VAL* 4.2 2.5 - - - -
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C GLU* 3.5 13.7 - - - +
60D GLY* 1.3 73.2 - - - -
62D LEU* 1.3 63.0 + - - +
63D ASN* 3.5 0.5 + - - -
76D LEU* 3.3 5.9 - - - -
77D ASN* 2.9 47.8 + - - +
78D ASP* 4.7 4.2 + - - +
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Residues in contact with LEU 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ARG* 3.0 18.0 + - - -
349C TRP* 3.6 46.7 - - + +
351C PHE* 4.3 5.6 - - + -
374C ALA* 3.6 12.7 - - + +
375C GLU 2.7 16.2 + - - +
376C TRP* 3.4 23.7 - - + +
61D SER* 1.3 72.3 + - - +
63D ASN* 1.3 59.7 + - - +
64D THR 3.3 23.3 - - - +
65D TYR* 4.1 11.2 - - + -
74D PHE* 3.9 11.0 - - + -
75D VAL 3.8 1.3 - - - +
76D LEU* 3.7 28.7 - - + -
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Residues in contact with ASN 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 3.9 7.5 + - - +
189A ASN* 3.6 0.9 - - - +
205A ARG* 3.0 26.2 + - - +
376C TRP* 3.6 4.2 + - - -
61D SER* 3.5 1.9 + - - +
62D LEU* 1.3 73.6 - - - +
64D THR* 1.3 78.1 + - - +
75D VAL* 2.9 25.5 + - + +
77D ASN* 2.7 31.6 + - - +
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Residues in contact with THR 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 3.1 40.9 + - - +
189A ASN* 3.2 16.4 - - - +
376C TRP* 4.5 0.4 - - - +
62D LEU* 3.3 13.1 - - - +
63D ASN* 1.3 97.3 - - - +
65D TYR* 1.3 64.4 + - - +
66D ARG* 6.0 2.4 + - - -
73D THR 5.2 0.9 + - - -
74D PHE* 3.4 1.6 - - - -
75D VAL* 3.2 44.1 + - - +
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Residues in contact with TYR 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ARG* 4.8 0.2 - - - -
189A ASN* 3.0 68.8 + - + -
190A ALA 3.7 4.7 - - - -
191A GLU* 3.8 20.1 + - + -
201A ILE 4.9 0.6 + - - -
202A MET 4.7 0.3 - - - -
203A ARG* 2.8 46.6 + - - +
349C TRP* 3.4 30.3 - + + -
376C TRP* 3.8 25.6 - + - -
62D LEU* 4.1 4.0 - - + -
64D THR* 1.3 77.8 - - - +
66D ARG* 1.3 65.0 + - - +
72D TRP* 4.2 7.6 - + + -
73D THR 3.4 8.5 - - - -
74D PHE* 3.6 23.3 - - + -
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Residues in contact with ARG 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA 3.0 22.7 + - - +
185A LEU* 2.9 34.7 + - - +
186A ARG* 3.7 9.7 + - - +
187A ALA 3.0 23.2 + - - +
188A ARG* 4.4 7.6 - - - +
190A ALA 3.2 11.4 - - - +
64D THR* 6.0 2.0 + - - -
65D TYR* 1.3 77.9 + - - +
67D PHE* 1.3 69.0 + - - +
68D CYS* 4.7 6.5 - - - +
71D VAL 3.6 2.2 - - - +
72D TRP* 3.3 11.0 - - - -
73D THR* 3.0 53.3 + - - +
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Residues in contact with PHE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ALA* 4.8 1.2 - - - +
190A ALA 3.0 6.6 + - - +
191A GLU* 3.5 13.9 - - + -
192A TYR* 2.9 38.5 + - - +
193A ASN* 3.8 32.3 - - + -
339C TYR* 3.6 7.0 - + - -
66D ARG* 1.3 78.0 - - - +
68D CYS* 1.3 63.5 + - - +
70D ASN* 3.5 45.3 - - - -
71D VAL 3.5 7.4 - - - -
72D TRP* 3.2 58.1 - + + -
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Residues in contact with CYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LYS* 4.5 8.3 - - - -
184A ALA* 3.7 31.0 - - + +
185A LEU* 3.8 33.2 - - + -
192A TYR* 3.7 21.3 - - - -
66D ARG* 4.7 4.7 - - + +
67D PHE* 1.3 76.3 - - - +
69D ASP* 1.3 81.1 + - - +
70D ASN 3.0 2.2 - - - +
71D VAL* 2.8 21.0 + - - +
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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