Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 1RM1
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 LYS 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A VAL 3.5 5.8 - - - +
75A THR* 3.4 37.0 + - + +
116A PHE* 2.9 31.5 + - - +
118A SER* 3.3 16.7 + - - +
119A GLY* 1.3 82.0 - - - +
121A MET* 1.3 61.0 + - - +
16D A 3.8 36.3 + - - +
17D C 3.8 18.9 + - - +
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Residues in contact with MET 121 (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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72A ALA 4.0 0.2 - - - +
73A THR* 3.3 6.4 - - - +
74A VAL* 2.9 55.7 + - + +
76A LEU* 4.2 22.0 - - + -
113A ALA* 4.5 4.5 - - - -
114A LEU 3.0 20.2 - - - +
115A ILE* 3.9 20.6 - - + -
116A PHE* 4.6 1.6 - - - -
120A LYS* 1.3 76.8 - - - +
122A VAL* 1.3 64.7 + - - +
123A VAL* 3.9 19.1 - - + -
136A SER* 3.4 17.9 - - - +
139A TYR* 3.4 33.9 - - + -
140A ALA 4.2 3.4 - - - +
16D A 5.3 1.2 - - - +
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Residues in contact with VAL 122 (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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71A VAL* 3.7 19.1 - - + -
72A ALA 3.3 5.4 - - - +
73A THR* 4.1 10.5 - - + -
112A THR 3.7 1.0 - - - +
113A ALA* 3.2 4.3 - - - +
114A LEU* 2.8 45.0 + - + +
116A PHE* 4.7 3.4 - - + -
121A MET* 1.3 79.1 - - - +
123A VAL* 1.3 64.6 + - - +
124A THR* 3.8 13.2 - - + +
15D A 3.6 26.7 - - + +
16D A 3.6 37.9 - - - +
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Residues in contact with VAL 123 (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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70A ILE 3.5 2.6 - - - +
71A VAL* 3.4 4.0 - - - -
72A ALA* 2.7 42.0 + - + +
74A VAL* 4.8 2.9 - - + -
111A THR* 4.1 15.3 - - + +
112A THR 3.7 2.2 - - - +
113A ALA* 4.4 1.6 - - + +
121A MET* 3.9 23.3 - - + -
122A VAL* 1.3 77.9 - - - +
124A THR* 1.3 64.4 + - - +
126A ALA* 5.5 1.1 - - + -
132A SER* 4.6 7.5 + - - +
135A ALA* 4.2 11.0 - - + -
136A SER* 3.2 28.5 - - - +
139A TYR* 3.9 27.1 - - + -
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Residues in contact with THR 124 (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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70A ILE 3.7 5.6 - - - -
71A VAL* 4.1 13.0 - - + -
111A THR* 3.2 9.1 - - - -
112A THR* 2.9 40.6 + - - +
114A LEU* 5.5 2.5 - - + -
122A VAL* 3.8 17.3 - - + +
123A VAL* 1.3 79.0 - - - +
125A GLY* 1.3 59.0 + - - +
126A ALA 3.3 5.6 - - - -
22E T 3.6 25.6 + - - +
23E T 3.0 36.8 + - - +
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Residues in contact with GLY 125 (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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68A GLN 4.4 2.4 - - - +
69A ASN* 2.9 23.8 + - - -
70A ILE 3.7 0.6 + - - -
110A LYS* 3.6 17.1 + - - +
111A THR* 4.7 0.9 - - - -
124A THR* 1.3 73.8 - - - +
126A ALA* 1.3 65.9 + - - +
127A LYS* 3.6 10.7 + - - +
23E T 3.4 21.1 - - - -
24E T 4.2 8.4 + - - +
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Residues in contact with ALA 126 (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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69A ASN* 3.2 3.3 - - - -
70A ILE* 2.6 41.2 + - + +
109A PRO* 6.0 0.2 - - - -
110A LYS 4.8 0.4 - - - -
111A THR* 3.7 17.6 - - + +
123A VAL* 5.5 2.2 - - + -
124A THR 3.3 4.4 + - - -
125A GLY* 1.3 79.0 - - - +
127A LYS* 1.3 59.5 + - - +
128A SER 3.5 2.5 - - - +
131A ASP* 4.2 4.3 - - + -
132A SER* 3.6 42.6 - - - +
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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