Contacts of the strand formed by residues 63 - 79 (chain A) in PDB entry 2NMU
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 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.6 1.6 - - - +
53A ALA* 3.5 3.8 - - - -
54A LEU* 2.7 40.2 + - - +
56A TYR* 3.5 44.6 + - + +
61A ALA 4.0 3.9 + - - -
62A THR* 1.3 72.2 - - - +
64A SER* 1.3 63.8 + - - +
65A LEU* 4.1 21.3 + - + +
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Residues in contact with SER 64 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A VAL 3.4 4.7 - - - -
53A ALA* 4.9 5.2 - - - +
62A THR* 4.0 11.3 + - - +
63A THR* 1.3 78.5 + - - +
65A LEU* 1.3 69.4 + - - +
66A THR* 5.6 0.2 - - - -
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Residues in contact with LEU 65 (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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50A THR 4.4 0.4 - - - -
51A ASP* 3.3 4.3 - - - +
52A VAL* 2.7 49.9 + - + +
54A LEU* 5.1 4.9 - - + -
56A TYR* 4.1 12.1 - - - +
63A THR* 4.2 16.8 - - + +
64A SER* 1.3 82.4 - - - +
66A THR* 1.3 64.1 + - - +
69A PHE* 4.1 20.4 - - + -
89A VAL* 5.8 0.7 - - + -
97A LEU* 3.6 31.2 - - + -
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Residues in contact with THR 66 (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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50A THR* 3.3 16.8 - - + +
51A ASP* 2.8 24.5 + - - +
65A LEU* 1.3 76.9 + - - +
67A GLY* 1.3 62.0 + - - +
69A PHE* 3.9 6.0 - - - -
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Residues in contact with GLY 67 (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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49A LEU 3.8 0.2 - - - +
50A THR* 2.9 34.5 + - - +
66A THR* 1.3 79.9 - - - +
68A THR* 1.3 64.1 + - - -
69A PHE* 3.6 8.4 - - - -
108A ARG* 4.4 2.3 - - - -
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Residues in contact with THR 68 (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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67A GLY* 1.3 73.3 + - - -
69A PHE* 1.3 64.9 + - - +
90A SER 4.1 0.2 - - - +
91A ASP* 3.7 3.5 - - - -
92A PRO* 3.3 42.1 - - + +
108A ARG* 3.5 36.9 - - - +
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Residues in contact with PHE 69 (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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48A SER* 3.2 0.3 - - - -
49A LEU* 2.9 37.0 + - + +
50A THR 3.7 12.6 - - - -
52A VAL* 3.5 26.5 - - + -
65A LEU* 4.1 22.2 - - + -
66A THR 3.9 5.8 - - - -
67A GLY* 3.6 25.4 - - - -
68A THR* 1.3 78.3 - - - +
70A GLU* 1.3 60.8 + - - +
89A VAL* 3.8 32.1 - - + -
90A SER 3.4 13.2 - - - +
91A ASP* 4.2 15.0 - - + -
95A VAL 6.0 0.2 - - - -
97A LEU* 4.7 12.8 - - + -
108A ARG* 3.2 15.6 + - - +
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Residues in contact with GLU 70 (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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47A GLY 3.6 10.5 - - - +
48A SER* 3.5 6.5 - - - -
69A PHE* 1.3 74.1 - - - +
71A VAL* 1.3 63.7 + - - +
72A ILE* 3.4 7.5 + - + -
89A VAL* 3.2 8.7 - - - +
90A SER* 3.0 47.5 + - - +
91A ASP 6.0 1.3 - - - +
108A ARG* 2.7 29.8 + - - +
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Residues in contact with VAL 71 (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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45A CYS* 4.1 22.9 - - - +
46A THR* 4.4 6.9 + - - -
47A GLY 2.8 32.8 + - - +
48A SER 4.2 0.2 - - - +
49A LEU* 3.5 39.3 - - + -
70A GLU* 1.3 73.3 - - - +
72A ILE* 1.3 62.6 + - - +
73A SER 3.9 15.0 - - - +
74A LEU* 4.3 1.3 - - + -
87A LEU* 3.8 20.0 - - + -
88A ALA 3.9 3.1 - - - -
89A VAL* 4.4 1.1 - - - -
101A MSE 6.1 0.2 - - + -
111A LEU* 3.8 16.6 - - + -
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Residues in contact with ILE 72 (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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45A CYS 4.5 7.1 - - - +
70A GLU* 4.4 6.1 - - + +
71A VAL* 1.3 78.1 - - - +
73A SER* 1.3 67.5 + - - +
88A ALA* 2.9 10.7 + - + +
90A SER* 3.3 38.4 - - - +
96A MSE 3.5 36.8 - - + -
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Residues in contact with SER 73 (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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45A CYS 5.1 4.0 - - - -
71A VAL* 3.6 3.6 - - - -
72A ILE* 1.3 86.5 - - - +
74A LEU* 1.3 61.6 + - - +
75A ASN* 3.9 18.6 + - - -
86A HIS 4.5 0.4 - - - -
87A LEU* 3.5 5.5 - - - +
88A ALA* 2.9 45.0 + - - +
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.6 7.2 - - + -
28A LEU* 5.0 5.2 - - + -
42A ILE* 3.3 29.6 - - + +
44A GLY* 5.8 0.2 - - - -
45A CYS* 3.7 36.5 + - - +
71A VAL* 4.3 5.6 - - + +
73A SER* 1.3 76.2 - - - +
75A ASN* 1.3 64.1 + - - +
85A LEU* 4.2 17.0 - - + -
86A HIS 3.4 15.7 - - - +
87A LEU* 4.5 4.0 - - + -
101A MSE 3.5 35.4 - - + -
111A LEU* 4.4 11.7 - - + -
113A LEU* 4.1 13.0 - - + -
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Residues in contact with ASN 75 (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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42A ILE* 4.2 13.8 - - - +
73A SER* 3.9 25.1 + - - -
74A LEU* 1.3 76.9 - - - +
76A GLY* 1.3 60.0 + - - +
85A LEU* 3.2 8.9 - - - +
86A HIS* 2.8 43.1 + - + +
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Residues in contact with GLY 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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41A TRP* 3.2 7.0 - - - +
42A ILE* 3.0 29.5 + - - +
75A ASN* 1.3 79.0 + - - +
77A THR* 1.3 64.7 + - - -
84A HIS 3.1 12.1 - - - -
85A LEU* 3.6 5.8 - - - -
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Residues in contact with THR 77 (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 ALA 3.3 8.7 - - - +
41A TRP* 4.4 7.4 - - + -
76A GLY* 1.3 78.1 - - - +
78A LEU* 1.3 66.7 + - - +
83A GLU* 3.3 1.0 - - - +
84A HIS* 2.9 32.8 + - - +
85A LEU* 3.8 2.8 - - - +
123A PHE* 3.9 23.8 - - + -
125A ARG* 2.8 31.0 + - - -
136A LEU* 4.6 14.1 - - + +
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Residues in contact with LEU 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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28A LEU* 4.2 32.5 - - + +
29A HIS* 6.1 2.0 - - - +
32A VAL* 3.6 26.5 - - + -
40A ALA* 2.9 59.2 + - + +
41A TRP* 3.7 10.5 - - - +
42A ILE* 4.0 19.7 - - + -
76A GLY 4.5 0.2 - - - +
77A THR* 1.3 80.3 - - - +
79A GLU* 1.3 71.5 + - - +
82A GLY 3.5 5.2 - - - +
83A GLU* 3.7 13.2 - - + -
85A LEU* 4.9 4.0 - - + -
115A ILE* 4.6 7.9 - - + -
123A PHE* 4.2 0.5 - - - -
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Residues in contact with GLU 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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29A HIS* 5.5 4.2 + - - -
32A VAL* 3.5 14.8 - - - +
37A LEU* 3.8 7.2 - - - -
38A ARG* 3.4 25.1 - - - +
78A LEU* 1.3 82.5 + - - +
80A LEU* 1.3 69.7 + - - +
81A THR* 4.1 7.2 - - - +
82A GLY* 2.8 42.5 + - - +
123A PHE* 3.5 32.0 - - + +
124A SER* 4.7 2.1 - - - -
125A ARG* 2.9 44.3 + - - +
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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