Contacts of the strand formed by residues 111 - 119 (chain B) in PDB entry 1NMS
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B TYR* 3.9 3.4 - - - -
43B GLU* 3.3 31.9 + - + +
45B GLY* 3.8 24.2 - - - -
46B LEU* 3.7 21.5 - - - +
84B GLU* 4.3 5.7 + - - -
86B ARG* 4.1 4.6 - - - +
106B GLU* 2.9 31.3 + - - +
107B ASP 3.9 15.4 + - - +
108B HIS* 3.0 49.8 + - + +
109B SER 3.2 0.2 - - - -
110B LYS* 1.3 82.0 - - + +
112B SER* 1.3 63.7 + - - +
113B SER 3.4 5.4 - - - +
151B LEU* 5.3 0.2 - - + -
154B LYS* 2.9 26.9 + - - +
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LYS 3.9 4.3 - - - +
39B MET* 3.3 40.1 + - - +
41B TYR* 3.2 35.7 + - - +
43B GLU 2.8 14.8 + - - -
44B MET* 3.3 11.3 + - - -
111B ARG* 1.3 73.6 - - - +
113B SER* 1.3 60.5 + - - +
154B LYS* 3.4 22.3 - - - +
155B PRO* 3.5 7.4 - - - +
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B MET* 3.9 8.5 - - - +
44B MET 2.7 24.8 + - - +
45B GLY* 3.4 13.7 - - - -
46B LEU 4.1 0.9 + - - -
83B TYR* 2.8 27.5 + - - -
108B HIS* 5.2 0.9 + - - -
111B ARG* 3.4 4.1 - - - +
112B SER* 1.3 79.7 - - - +
114B PHE* 1.3 63.9 + - - +
115B VAL* 5.5 1.1 - - - -
151B LEU* 4.1 9.6 - - - +
154B LYS* 4.6 4.0 - - - +
155B PRO* 3.4 28.5 - - - -
157B LEU* 5.8 2.5 - - - -
273B LEU* 5.9 1.1 - - - -
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B LEU* 3.9 18.8 - - + -
48B ILE* 3.9 17.7 - - + -
100B MET* 4.9 3.1 - - + -
103B VAL* 3.5 24.9 - - + -
108B HIS* 4.2 12.6 - + - +
113B SER* 1.3 77.9 - - - +
115B VAL* 1.3 77.5 + - - +
116B CYS* 3.7 25.4 - - + -
143B PHE* 3.6 35.4 - + - -
151B LEU* 3.7 22.7 - - + -
155B PRO 3.0 7.1 + - - +
156B LYS* 3.5 6.8 - - + -
157B LEU* 2.9 26.3 + - - +
158B PHE* 4.0 18.2 - + - -
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Residues in contact with VAL 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU 2.9 13.4 + - - +
47B CYS* 3.3 24.0 - - + -
48B ILE 2.9 23.4 + - - -
78B PHE* 4.1 10.5 - - + -
83B TYR* 3.6 30.1 - - + +
113B SER* 4.9 0.2 - - - +
114B PHE* 1.3 89.0 - - - +
116B CYS* 1.3 64.2 + - - +
117B VAL* 4.1 4.3 - - + -
157B LEU* 3.4 26.2 - - + +
159B ILE* 4.0 27.1 - - + -
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Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 3.4 9.9 - - + +
50B ILE* 4.8 1.6 - - - -
100B MET* 4.1 25.8 - - - -
114B PHE* 3.7 11.9 - - + -
115B VAL* 1.3 76.0 - - - +
117B VAL* 1.3 64.2 + - - +
118B LEU* 3.7 30.1 + - - +
139B ILE* 5.1 0.4 - - - -
157B LEU 2.8 6.7 + - - -
158B PHE* 3.3 30.6 - - + +
159B ILE* 2.9 25.1 + - - +
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B CYS* 4.2 11.9 - - - -
48B ILE 2.7 16.4 + - - +
49B ILE* 4.3 12.1 - - + -
50B ILE 2.8 28.4 + - - +
74B LEU* 3.7 33.4 - - + -
78B PHE* 4.9 0.9 - - + -
115B VAL* 4.1 14.8 - - + -
116B CYS* 1.3 78.8 - - - +
118B LEU* 1.3 67.1 + - - +
119B LEU* 3.8 15.7 - - + -
159B ILE* 3.3 33.4 - - + +
216B ILE* 4.6 1.1 - - + -
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 3.6 36.6 - - + -
96B ILE* 5.2 2.5 - - + -
116B CYS* 3.7 18.6 - - - +
117B VAL* 1.3 79.2 - - - +
119B LEU* 1.3 64.2 + - - +
120B SER 4.0 0.4 - - - -
127B ILE* 4.0 26.7 - - + -
136B LEU* 3.6 31.2 - - + -
139B ILE* 4.3 20.0 - - + -
158B PHE* 5.2 3.6 - - + -
159B ILE 2.8 12.7 + - - +
160B ILE* 4.5 12.2 - - + +
161B GLN 2.9 28.5 + - - +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ILE* 4.2 9.2 - - + -
50B ILE* 2.9 16.5 + - - +
51B ASN* 3.7 20.2 - - - +
52B ASN* 3.0 23.7 + - - +
64B ARG* 3.3 9.0 + - - +
67B THR* 3.7 16.4 - - - +
70B ASP* 4.1 6.7 - - + +
71B ALA* 4.1 26.7 - - - +
74B LEU* 4.2 12.3 - - + -
117B VAL* 3.8 20.0 - - + -
118B LEU* 1.3 80.0 - - - +
120B SER* 1.3 61.5 + - - +
161B GLN* 3.6 21.8 - - + -
216B ILE* 4.2 7.4 - - + -
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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