Contacts of the strand formed by residues 75 - 83 (chain A) in PDB entry 5NC5
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 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A MET 5.2 0.7 - - - +
72A ILE* 3.7 32.6 + - + +
73A ASP 3.2 1.6 + - - -
74A ASN* 1.3 77.6 - - - +
76A MET* 1.3 62.3 + - - +
77A TYR 3.3 28.0 - - - +
78A MET* 5.1 2.5 - - + -
92A LEU* 3.8 36.8 - - + -
93A THR 3.4 12.3 - - - +
94A PHE* 4.2 8.7 - - + -
95A GLU* 5.5 0.6 - - - +
820A ASN* 6.0 0.7 - - - +
168C ARG* 4.1 46.1 - - + +
170C SER* 5.5 6.6 + - - -
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Residues in contact with MET 76 (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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40A PRO* 4.5 9.0 - - + -
75A LEU* 1.3 76.8 - - - +
77A TYR* 1.3 89.8 + - + +
93A THR* 2.8 24.3 + - + +
94A PHE 3.8 18.6 - - - +
95A GLU* 3.2 50.0 - - - +
96A SER 5.2 0.4 - - - -
673A GLU* 6.0 0.7 - - - +
820A ASN* 4.4 6.9 + - - +
864A TYR* 3.6 35.8 + - + +
865A GLN* 5.4 7.6 - - - +
868A LEU* 5.9 1.3 - - - -
168C ARG 5.8 0.2 - - - +
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 5.5 1.2 - - - +
75A LEU* 3.3 10.4 - - - +
76A MET* 1.3 105.6 - - + +
78A MET* 1.3 64.2 + - - +
79A SER* 5.5 2.9 - - - -
93A THR* 2.9 52.9 + - + +
673A GLU* 4.7 5.7 + - - -
819A TYR* 3.4 29.6 - + + +
820A ASN* 3.7 16.4 - - - +
860A THR* 3.5 19.5 - - - -
861A GLY* 3.5 20.8 + - - -
864A TYR* 3.6 32.9 - + + +
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Residues in contact with MET 78 (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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66A GLU* 3.6 43.7 - - + +
69A MET* 4.1 22.7 - - - -
75A LEU* 5.1 1.8 - - + -
77A TYR* 1.3 78.4 - - - +
79A SER* 1.3 68.1 + - - +
90A ILE* 4.3 8.3 - - + -
91A THR 3.3 9.9 - - - +
92A LEU* 4.2 17.0 - - + -
819A TYR* 3.6 7.4 - - - -
820A ASN* 2.9 35.2 + - - +
821A GLY 4.1 7.6 - - - +
168C ARG* 3.8 38.4 - - - +
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Residues in contact with SER 79 (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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77A TYR* 5.5 3.3 - - - -
78A MET* 1.3 75.9 - - - +
80A SER* 1.3 68.5 + - - +
89A GLN 4.6 0.2 - - - -
90A ILE* 3.4 3.8 - - - +
91A THR* 2.8 45.7 + - - -
683A GLU* 5.7 2.2 - - - -
818A ARG 3.5 10.3 - - - -
819A TYR* 4.3 14.8 - - - -
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Residues in contact with SER 80 (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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62A THR* 3.7 13.1 - - - +
66A GLU* 3.5 21.8 + - - -
79A SER* 1.3 83.8 + - - +
81A ASN* 1.4 69.4 + - - +
82A SER* 4.5 0.5 + - - -
89A GLN 3.3 8.3 - - - -
90A ILE* 3.9 20.4 - - - -
816A LEU 3.5 1.7 - - - +
817A GLU* 3.4 3.1 - - - +
818A ARG* 3.1 35.6 + - - +
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Residues in contact with ASN 81 (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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80A SER* 1.4 80.5 + - - +
82A SER* 1.3 62.1 + - - +
83A ASP* 4.3 14.5 - - - +
87A THR* 3.8 1.6 - - - +
88A VAL* 3.4 5.5 - - - -
89A GLN* 3.1 38.9 + - + +
617A PHE 5.9 0.4 + - - -
618A ALA 3.9 11.2 + - - +
815A ARG* 3.1 40.3 + - + +
816A LEU 3.6 4.0 - - - +
817A GLU* 4.0 13.3 - - - +
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Residues in contact with SER 82 (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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54A ALA* 3.5 22.6 - - - +
57A VAL* 3.9 9.0 - - - -
58A GLN* 3.6 17.9 + - - -
62A THR* 3.4 29.0 + - - +
80A SER* 4.5 1.9 + - - -
81A ASN* 1.3 75.3 - - - +
83A ASP* 1.3 61.2 + - - +
87A THR 3.7 5.4 - - - -
88A VAL* 4.5 0.7 - - - +
815A ARG* 3.5 0.3 - - - -
816A LEU* 2.8 39.3 + - - -
818A ARG* 5.0 0.2 - - - -
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Residues in contact with ASP 83 (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 ASP 4.3 1.0 - - - +
54A ALA* 3.7 11.6 + - - +
57A VAL* 4.4 2.4 - - - +
81A ASN* 4.3 8.0 - - - +
82A SER* 1.3 75.6 - - - +
84A SER* 1.3 58.8 + - - +
85A THR* 2.7 31.6 + - - +
86A GLY* 3.0 21.7 + - - -
87A THR* 3.0 25.8 + - - +
618A ALA 4.0 18.5 - - - +
619A GLY 4.8 0.8 + - - -
620A ARG 5.3 3.8 - - - +
814A PRO 3.2 13.9 - - - +
815A ARG* 3.7 22.0 - - + +
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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