Contacts of the strand formed by residues 40 - 55 (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 ALA 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A LEU* 4.1 15.3 - - + -
39A ALA* 1.3 75.2 - - - +
41A TRP* 1.3 65.6 + - - +
77A THR* 3.3 3.3 - - - -
78A LEU* 2.9 48.9 + - + +
115A ILE* 4.0 10.5 - - + -
116A GLY 2.9 14.4 - - - +
117A GLU* 3.7 8.7 - - - +
123A PHE* 3.5 7.9 - - - -
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Residues in contact with TRP 41 (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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11A ALA* 4.0 7.4 - - + -
13A PHE* 3.8 34.5 - + - -
40A ALA* 1.3 77.6 - - - +
42A ILE* 1.3 84.6 + - - +
43A ALA* 3.2 18.7 + - + +
76A GLY 3.2 15.0 - - - +
77A THR* 4.3 10.3 - - + -
78A LEU* 3.8 6.3 - - - -
115A ILE* 3.6 4.0 - - - +
116A GLY* 2.9 58.9 + - - -
117A GLU 4.1 0.9 - - - -
118A LEU* 3.6 37.0 - - + -
123A PHE* 5.3 1.6 - - + -
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Residues in contact with ILE 42 (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* 4.7 8.7 - - + -
41A TRP* 1.3 80.4 - - - +
43A ALA* 1.3 60.6 + - - +
44A GLY 3.7 20.0 - - - +
45A CYS* 4.0 2.9 - - + -
74A LEU* 3.3 32.0 - - + +
75A ASN* 4.2 14.3 - - - +
76A GLY 3.0 10.2 + - - +
78A LEU* 4.0 20.2 - - + -
85A LEU* 3.7 28.3 - - + -
113A LEU* 4.0 21.1 - - + -
114A VAL 4.1 3.6 - - - +
115A ILE* 4.1 19.7 - - + +
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Residues in contact with ALA 43 (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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13A PHE* 3.9 26.7 - - + -
41A TRP* 3.2 23.3 + - + +
42A ILE* 1.3 74.3 - - - +
44A GLY* 1.3 57.1 + - - +
114A VAL* 2.9 22.6 + - + +
116A GLY 4.4 2.0 - - - +
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Residues in contact with GLY 44 (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* 3.4 6.9 - - - +
43A ALA* 1.3 80.5 - - - +
45A CYS* 1.3 63.9 + - - +
74A LEU 5.4 0.2 - - - -
112A GLU 4.5 0.2 - - - -
113A LEU* 3.4 1.8 - - - -
114A VAL* 2.9 38.4 + - - +
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Residues in contact with CYS 45 (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* 4.0 4.3 - - + -
44A GLY* 1.3 76.2 - - - +
46A THR* 1.3 68.1 + - - +
71A VAL* 4.1 8.5 - - - +
72A ILE 4.5 12.0 - - - +
73A SER* 5.1 2.3 - - - -
74A LEU* 3.7 38.3 + - + +
111A LEU* 3.7 19.1 - - - -
112A GLU 3.2 9.4 - - - -
113A LEU* 3.5 26.2 - - + -
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Residues in contact with THR 46 (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* 1.3 77.7 - - - +
47A GLY* 1.3 57.9 + - - +
71A VAL 4.4 9.7 + - - -
111A LEU* 3.5 6.1 - - - +
112A GLU* 2.7 66.8 + - + +
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Residues in contact with GLY 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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46A THR* 1.3 81.0 + - - +
48A SER* 1.3 61.7 + - - -
70A GLU* 3.6 11.6 - - - +
71A VAL* 2.8 30.4 + - - +
110A THR* 3.2 21.1 - - - -
111A LEU* 4.0 3.8 - - - -
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Residues in contact with SER 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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47A GLY* 1.3 74.6 - - - -
49A LEU* 1.3 72.0 + - - +
69A PHE 3.2 5.4 - - - -
70A GLU* 3.5 5.8 - - - -
71A VAL* 4.2 3.2 - - - +
107A VAL* 3.6 1.6 - - - +
108A ARG* 2.9 46.9 + - - +
109A THR* 2.6 43.1 + - - -
110A THR 2.9 10.4 + - - +
111A LEU* 4.5 0.5 - - - +
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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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24A VAL* 4.0 19.5 - - + -
48A SER* 1.3 82.4 - - - +
50A THR* 1.3 59.8 + - - +
51A ASP 3.9 6.1 - - - +
52A VAL* 4.1 13.0 - - + -
69A PHE* 2.9 36.0 + - + +
71A VAL* 3.5 25.1 - - + -
87A LEU* 3.9 27.1 - - + -
89A VAL* 4.1 9.2 - - + -
101A MSE 4.5 1.6 - - + -
105A CYS* 4.2 8.5 - - + -
106A THR 3.2 28.0 - - - +
107A VAL* 4.0 4.9 - - + -
108A ARG* 3.3 11.6 + - - +
111A LEU* 4.9 3.6 - - + -
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Residues in contact with THR 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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49A LEU* 1.3 71.5 - - - +
51A ASP* 1.3 76.2 + - - +
66A THR* 3.3 12.6 - - + -
67A GLY 2.9 38.5 + - - +
69A PHE* 3.7 7.2 - - - -
106A THR* 2.9 13.6 + - - -
107A VAL 4.4 2.0 + - - -
108A ARG* 3.5 29.0 - - - +
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Residues in contact with ASP 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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49A LEU* 3.9 2.1 - - - +
50A THR* 1.3 84.8 - - - +
52A VAL* 1.3 64.1 + - - +
65A LEU 3.3 5.4 - - - +
66A THR* 2.8 33.1 + - - +
104A GLY 3.5 15.9 - - - +
105A CYS* 3.2 4.5 - - - +
106A THR* 3.0 48.9 + - + +
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Residues in contact with VAL 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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49A LEU* 4.1 16.8 - - + -
51A ASP* 1.3 80.4 - - - +
53A ALA* 1.3 62.9 + - - +
54A LEU* 3.6 32.3 - - + +
63A THR 3.6 1.0 - - - +
64A SER* 3.4 4.2 - - - -
65A LEU* 2.7 53.7 + - + +
69A PHE* 3.5 34.5 - - + -
87A LEU* 4.0 14.4 - - + -
89A VAL* 4.4 10.1 - - + -
104A GLY 4.7 1.1 - - - -
105A CYS* 4.0 2.2 - - - -
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Residues in contact with ALA 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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52A VAL* 1.3 74.3 - - - +
54A LEU* 1.3 63.0 + - - +
62A THR* 4.1 8.3 - - + -
63A THR 3.5 5.8 - - - -
64A SER* 4.7 5.8 - - - +
101A MSE 3.9 1.0 - - - -
102A MSE 2.9 35.6 + - + +
103A PRO 3.2 28.3 - - - +
104A GLY* 3.9 9.2 - - - +
105A CYS* 3.3 11.5 - - - +
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Residues in contact with LEU 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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52A VAL* 3.6 22.9 - - + -
53A ALA* 1.3 76.3 - - - +
55A ARG* 1.3 57.8 + - - +
56A TYR* 3.9 31.0 - - + +
62A THR* 3.5 4.1 - - - +
63A THR* 2.7 44.7 + - - +
65A LEU* 5.1 4.5 - - + -
87A LEU* 3.8 33.2 - - + +
89A VAL* 4.9 3.4 - - + -
97A LEU* 4.5 11.0 - - + +
98A GLY* 4.1 17.9 - - - +
99A GLY* 3.8 24.7 - - - +
100A HIS 3.4 5.4 - - - +
101A MSE 4.2 1.3 - - - -
102A MSE 4.2 0.4 - - - -
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Residues in contact with ARG 55 (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 LEU* 1.3 73.4 - - - +
56A TYR* 1.3 67.6 + - - +
59A GLN 3.5 26.3 + - - +
60A GLU* 3.9 19.2 + - - -
61A ALA 3.6 18.6 - - - +
62A THR* 4.6 1.1 - - - +
100A HIS* 2.8 77.5 + - + +
102A MSE 3.9 26.0 - - + +
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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