Contacts of the strand formed by residues 109 - 116 (chain B) in PDB entry 1RPU
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 GLY 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64B GLY 4.3 0.3 - - - +
66B GLY* 3.2 25.4 + - - +
108B VAL* 1.3 72.7 - - - +
110B CYS* 1.3 63.4 + - - -
111B THR* 4.3 3.0 + - - -
125B GLY 3.8 1.6 - - - -
12C C 4.4 6.9 - - - +
13C G 2.9 34.1 + - - -
8D G 4.7 9.3 + - - +
9D U 5.2 2.8 + - - -
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Residues in contact with CYS 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B TRP* 5.5 0.7 - - + -
64B GLY 3.2 7.9 - - - +
65B PHE* 4.0 26.7 - - + -
99B ALA* 6.0 0.4 - - - -
108B VAL* 4.0 8.1 - - - -
109B GLY* 1.3 74.1 - - - -
111B THR* 1.3 73.0 + - - +
124B SER* 3.8 0.5 - - - -
125B GLY 2.8 33.6 + - - +
127B SER* 3.8 28.7 - - - -
130B LEU* 4.5 14.8 - - + -
133B LEU* 3.8 14.8 - - + -
12C C 4.1 1.9 + - - -
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Residues in contact with THR 111 (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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62B SER* 4.4 1.1 - - - +
63B TRP* 3.2 15.4 - - - -
64B GLY* 2.9 34.7 + - - +
109B GLY 4.3 3.9 + - - -
110B CYS* 1.3 84.8 + - - +
112B TYR* 1.3 65.7 + - - +
122B THR* 3.7 14.6 - - + -
123B ILE 3.3 9.6 - - - +
124B SER* 4.1 7.0 + - - +
133B LEU* 4.7 1.5 - - - +
12C C 5.1 5.4 + - - -
9D U 5.4 0.9 + - - -
10D C 2.7 54.8 + - + +
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Residues in contact with TYR 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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61B GLU* 2.6 42.0 + - + +
62B SER 3.3 12.3 - - - -
63B TRP* 3.4 47.1 - + + -
90B TRP* 3.3 16.9 + + - -
111B THR* 1.3 78.0 - - - +
113B SER* 1.3 64.5 + - - +
114B ILE* 3.8 26.0 - - + +
121B VAL 3.7 1.0 - - - +
122B THR* 3.1 4.2 - - - +
123B ILE* 2.7 44.1 + - + +
133B LEU* 6.2 0.4 - - + -
137B ALA* 3.4 37.9 - - + -
140B SER* 5.7 1.1 - - - -
141B LYS* 3.6 11.7 - - + +
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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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60B LYS 4.5 0.2 - - - -
61B GLU* 3.1 4.7 - - - +
62B SER* 2.9 37.1 + - - -
112B TYR* 1.3 74.2 - - - +
114B ILE* 1.3 63.7 + - - +
120B SER* 5.4 1.3 - - - -
121B VAL 3.1 6.5 - - - -
122B THR* 2.8 22.5 + - - +
10D C 2.4 27.2 + - - -
11D A 3.1 25.1 - - - -
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Residues in contact with ILE 114 (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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59B PHE* 3.9 25.1 - - + -
60B LYS 3.2 13.2 - - - +
61B GLU* 4.3 0.7 - - + -
112B TYR* 3.8 25.6 - - + +
113B SER* 1.3 78.0 - - - +
115B ARG* 1.3 66.7 + - - +
120B SER* 3.3 3.4 - - - -
121B VAL* 2.9 42.5 + - + +
140B SER* 5.3 0.2 - - - -
141B LYS* 3.8 39.9 - - + +
144B LEU* 3.8 23.6 - - + +
145B LEU* 4.4 10.1 - - + -
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Residues in contact with ARG 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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59B PHE* 3.4 19.0 - - - +
60B LYS* 3.0 22.5 + - + +
114B ILE* 1.3 76.9 - - - +
116B PHE* 1.3 64.8 + - - +
118B GLY* 4.0 26.3 + - - +
119B VAL 3.3 15.7 - - - +
120B SER* 4.2 4.5 - - - -
144B LEU* 4.5 0.7 - - - -
1C C 6.1 0.7 - - - -
11D A 5.6 0.4 - - - +
12D C 3.1 57.7 + - - +
13D G 2.8 26.7 + - - -
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Residues in contact with PHE 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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56B PRO* 3.4 25.8 - - + -
58B GLY* 3.5 21.8 - - - -
59B PHE* 3.8 7.9 - - + -
76B TYR* 3.5 36.1 - + + -
78B ARG* 4.0 20.9 - - + -
115B ARG* 1.3 75.3 - - - +
117B ARG* 1.3 95.7 + - + +
118B GLY 3.4 1.6 - - - -
119B VAL* 3.0 22.1 + - - +
144B LEU* 3.8 27.8 - - + +
145B LEU* 3.7 31.0 - - + -
147B LEU* 5.1 2.3 - - + +
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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