Contacts of the strand formed by residues 95 - 101 (chain A) in PDB entry 4IRP
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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A ARG* 1.3 72.7 - - - +
96A ALA* 1.3 64.4 + - - +
97A VAL* 3.7 23.6 - - + -
119A LEU* 4.0 23.1 - - + -
124A ILE* 4.0 11.7 - - + -
125A ARG 2.7 17.0 + - - +
126A HIS* 3.1 4.0 - - + +
127A HIS 3.0 24.9 + - - -
156A THR* 3.9 3.7 - - - +
158A TYR* 3.6 31.2 - - + +
159A ILE 3.5 7.4 - - - -
160A ALA* 3.5 32.8 - - + +
175A TYR* 4.4 18.4 - - + +
205A LEU* 4.8 0.7 - - + -
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Residues in contact with ALA 96 (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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95A LEU* 1.3 71.0 - - - +
97A VAL* 1.3 63.1 + - - +
98A LEU* 3.4 12.6 + - + +
127A HIS 3.7 4.7 - - - -
129A TYR* 4.0 5.4 - - + -
152A SER* 4.0 20.0 - - - +
156A THR* 3.5 28.5 - - + +
158A TYR 2.9 15.3 + - - +
159A ILE 3.4 1.6 - - - +
160A ALA 2.9 24.8 + - - -
208A LYS* 5.1 2.5 - - - -
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Residues in contact with VAL 97 (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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95A LEU* 3.7 28.5 - - + -
96A ALA* 1.3 69.9 - - - +
98A LEU* 1.3 61.8 + - - +
99A VAL* 3.6 13.5 + - + +
111A PHE* 4.2 11.4 - - + -
115A MET* 5.4 3.6 - - + -
119A LEU* 4.1 13.7 - - + -
126A HIS* 4.3 3.6 - - + -
127A HIS 3.0 15.8 - - - -
128A ILE* 3.7 17.2 - - + -
129A TYR* 2.9 29.5 + - - +
160A ALA* 3.7 5.6 - - + +
162A HIS* 3.9 30.3 - - + -
175A TYR* 6.3 0.2 - - + -
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Residues in contact with LEU 98 (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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96A ALA* 3.8 17.9 - - + +
97A VAL* 1.3 78.4 - - - +
99A VAL* 1.3 59.3 + - - +
100A PRO* 3.4 5.0 - - - +
129A TYR* 3.8 21.8 - - + -
131A LEU* 3.7 10.8 - - + -
145A ILE* 3.9 25.9 - - + +
148A GLY* 3.8 26.0 - - - +
149A PHE* 3.7 27.6 - - + +
152A SER* 4.7 0.2 - - - -
159A ILE 5.7 2.2 - - - -
160A ALA 2.7 16.7 + - - +
161A MET* 3.7 7.8 - - + -
162A HIS 3.0 24.3 + - - +
211A TYR* 6.2 0.2 - - + -
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Residues in contact with VAL 99 (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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97A VAL* 4.0 11.4 - - + -
98A LEU* 1.3 74.5 - - - +
100A PRO* 1.3 67.1 - - - +
101A PHE* 3.4 6.0 + - + +
108A LEU* 5.3 2.7 - - + -
111A PHE* 3.4 30.5 - - + -
128A ILE* 4.1 9.9 - - + -
129A TYR 2.8 18.9 + - - +
130A VAL* 3.6 7.4 - - + -
131A LEU* 2.8 26.1 + - - +
162A HIS 3.6 10.5 - - - +
164A VAL* 3.6 38.6 - - + -
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Residues in contact with PRO 100 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU 3.4 11.7 - - - +
99A VAL* 1.3 87.0 - - - +
101A PHE* 1.3 60.5 + - - +
131A LEU* 3.5 15.0 - - + +
139A PHE* 4.1 12.3 - - + -
141A ARG* 3.9 41.1 - - + +
144A LEU* 4.1 16.4 - - + -
145A ILE* 4.6 8.5 - - + -
162A HIS 3.5 14.4 - - - +
163A ASP* 5.2 0.2 - - - +
401A UDP 2.9 32.3 + - - +
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Residues in contact with PHE 101 (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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99A VAL* 3.6 2.7 - - + +
100A PRO* 1.3 77.7 - - - +
102A ARG* 1.3 64.4 + - - +
103A GLU 4.0 6.3 - - - -
104A ARG* 3.3 54.3 - - + -
105A PHE* 3.7 7.2 - - - -
108A LEU* 3.8 24.9 - - + -
130A VAL* 3.6 27.4 - - + -
131A LEU 2.8 22.8 + - - +
132A ASN* 3.7 14.2 - - - +
133A GLN 3.5 14.2 + - - -
139A PHE* 3.6 9.2 - - - -
164A VAL* 4.3 13.5 - - + -
401A UDP 3.3 3.8 - - - -
105B PHE* 3.5 28.5 - + + -
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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