Contacts of the strand formed by residues 109 - 116 (chain B) in PDB entry 1RRP
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 SER 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A LEU* 5.5 4.0 - - - +
102B PRO 3.4 11.5 - - - +
103B ASN* 3.6 11.1 + - - +
106B SER* 2.7 42.6 + - - +
107B ASP 3.7 0.8 - - - -
108B ARG* 1.3 81.0 - - - +
110B PHE* 1.3 72.6 + - - +
128B ALA* 6.0 2.0 - - - -
129B ILE 2.8 20.4 - - - -
130B ARG* 3.3 22.6 + - - +
131B PHE* 5.1 0.2 - - - -
137B ALA* 4.5 1.0 - - - +
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Residues in contact with PHE 110 (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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100B LEU* 4.1 30.5 - - + -
101B THR 3.2 11.9 - - - +
102B PRO* 3.2 19.1 - - + -
103B ASN* 5.0 1.6 - - - -
106B SER 5.4 1.6 - - - -
107B ASP* 5.4 4.7 - - - -
109B SER* 1.3 83.0 - - - +
111B VAL* 1.3 61.6 + - - +
112B TRP* 3.8 3.0 - - - -
128B ALA* 3.0 4.5 - - - +
129B ILE* 2.8 47.4 + - + +
131B PHE* 4.0 4.5 - + - -
137B ALA* 3.4 49.8 - - + -
138B ALA* 4.4 0.7 - - - -
140B PHE* 3.8 19.7 - + - -
141B LYS* 4.0 23.8 - - + -
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Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 3.8 22.5 - - + +
204A ALA* 5.0 0.9 - - + -
205A GLN* 3.7 32.1 - - + +
57B TRP* 4.3 15.3 - - + -
99B LYS 3.5 0.9 - - - +
100B LEU* 4.5 0.7 - - - -
101B THR* 3.0 42.5 + - - +
102B PRO 3.4 15.7 - - - +
103B ASN* 4.3 4.0 - - + +
110B PHE* 1.3 77.3 - - - +
112B TRP* 1.3 64.2 + - - +
127B LEU 2.7 23.1 - - - +
128B ALA* 4.4 5.8 - - + -
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Residues in contact with TRP 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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201A LEU* 4.2 8.1 - - - -
47B LEU* 4.0 16.4 - - + -
78B LEU* 4.3 19.2 - - + +
90B ALA* 5.9 1.3 - - + -
92B HIS* 3.1 33.8 + + - -
98B MET* 4.3 13.7 - - + -
99B LYS 4.0 18.4 - - - +
100B LEU* 3.5 31.4 - - + -
110B PHE 3.8 9.0 - - - -
111B VAL* 1.3 79.8 - - - +
113B HIS* 1.3 68.2 + - - +
114B ALA* 3.8 6.2 - - + +
127B LEU* 2.7 65.9 + - + +
129B ILE* 3.7 33.9 - - + -
140B PHE* 5.3 3.1 - + - -
144B PHE* 4.7 3.5 - + - -
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Residues in contact with HIS 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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197A TYR* 3.4 46.8 - + + +
201A LEU* 3.6 29.7 - - + +
98B MET* 3.6 20.1 - - - +
99B LYS 5.8 0.2 - - - +
112B TRP* 1.3 77.9 - - - +
114B ALA* 1.3 81.2 + - - +
115B LEU* 4.8 2.0 + - - +
124B PRO* 3.3 46.4 - - + +
125B GLU 3.1 14.0 + - - -
126B GLN* 4.2 5.2 - - + +
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Residues in contact with ALA 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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92B HIS* 3.4 33.2 - - + +
98B MET* 3.4 21.3 - - + -
112B TRP* 3.8 6.9 + - - +
113B HIS* 1.3 89.4 + - - +
115B LEU* 1.3 57.4 + - - +
116B ASP* 2.8 10.7 + - - +
125B GLU 3.1 27.5 + - - +
127B LEU* 4.6 3.1 - - + -
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Residues in contact with LEU 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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185A PRO* 4.0 22.9 - - + +
187A VAL* 3.9 34.3 - - + -
92B HIS* 4.1 9.8 - - - +
98B MET* 4.5 4.9 - - - +
113B HIS* 4.5 2.5 + - + +
114B ALA* 1.3 69.5 - - - +
116B ASP* 1.3 64.5 + - - +
122B PRO* 3.5 24.7 - - + +
123B LYS 3.3 35.9 - - - +
124B PRO* 3.5 14.8 - - + -
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Residues in contact with ASP 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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60B ARG* 5.8 0.4 - - - -
89B CYS 5.1 0.7 - - - -
90B ALA* 3.1 8.4 - - - -
91B ASN 2.7 24.0 + - - -
92B HIS* 2.8 29.7 - - + -
114B ALA 2.8 11.5 + - - +
115B LEU* 1.3 74.6 - - - +
117B TYR* 1.3 60.0 + - - +
118B ALA* 2.4 41.4 + - - +
121B LEU 3.7 0.9 - - - +
122B PRO* 3.4 2.1 - - - +
123B LYS* 2.9 29.6 + - - +
125B GLU* 3.5 25.1 - - - +
127B LEU* 4.7 7.0 - - + +
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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