Contacts of the strand formed by residues 114 - 122 (chain A) in PDB entry 5IHB
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 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A ARG* 4.1 7.4 - - - -
112A ASP 3.4 0.6 + - - -
113A ASN* 1.3 76.7 - - - +
115A SER* 1.3 61.4 + - - -
116A TYR* 3.4 11.4 - - - -
135A SER* 3.4 4.8 - - - -
136A VAL 2.9 32.8 + - - -
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Residues in contact with SER 115 (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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62A ARG* 3.6 8.2 + - - +
63A GLU* 2.8 53.2 + - - +
114A GLY* 1.3 71.9 - - - -
116A TYR* 1.3 60.3 + - - +
133A GLN* 3.6 14.6 + - - +
134A LEU 3.3 6.0 - - - -
135A SER* 4.1 13.7 + - - -
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Residues in contact with TYR 116 (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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60A TRP* 4.0 19.8 - - + -
61A PHE 3.0 17.0 - - - +
62A ARG* 3.4 43.8 + - + -
63A GLU 4.3 0.4 - - - +
73A VAL* 4.0 18.6 - - + +
86A THR* 5.4 1.0 - - - +
90A PHE* 3.8 30.2 - + - -
103A LEU* 5.4 4.5 - - + -
112A ASP* 2.8 27.2 + - - -
114A GLY 3.4 21.1 - - - -
115A SER* 1.3 75.4 - - - +
117A PHE* 1.3 62.2 + - - +
133A GLN* 3.4 8.4 - - - +
134A LEU* 2.7 44.3 + - + +
136A VAL* 3.6 17.9 - - + -
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Residues in contact with PHE 117 (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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59A TYR 3.8 0.2 - - - +
60A TRP* 3.5 8.4 - - - -
61A PHE* 2.9 73.5 + + + -
62A ARG 3.6 11.0 - - - -
63A GLU* 4.0 13.9 - - - -
65A ALA* 4.7 0.4 - - + -
66A ILE* 3.6 41.7 - - + -
116A TYR* 1.3 73.3 - - - +
118A PHE* 1.3 69.8 + - - +
119A ARG* 4.6 0.9 - - + -
128A SER* 3.5 30.1 - - - -
129A TYR 3.5 17.5 - - - +
130A LYS* 5.9 1.1 - - + -
132A PRO 5.5 0.9 - - - -
133A GLN* 3.9 19.7 - - + +
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Residues in contact with PHE 118 (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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23A LEU* 4.0 19.6 - - + +
43A PHE* 3.7 34.8 - + - -
58A GLY* 3.8 14.1 - - - -
59A TYR 3.3 26.5 - - - -
60A TRP* 3.5 40.1 - + + -
92A LEU* 4.3 7.0 - - + -
96A PRO* 5.0 2.5 - - + -
101A CYS* 3.5 24.0 - - + -
117A PHE* 1.3 76.6 - - - +
119A ARG* 1.3 75.0 + - - +
120A MET* 4.0 7.4 - - + -
128A SER* 3.7 1.4 - - - -
129A TYR* 3.0 45.7 + + - +
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Residues in contact with ARG 119 (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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58A GLY* 3.4 4.5 - - - -
59A TYR* 2.7 47.2 + - + +
61A PHE* 3.8 30.0 - - + -
118A PHE* 1.3 79.7 - - - +
120A MET* 1.3 67.6 + - - +
121A GLU* 2.8 27.0 + - - -
126A LYS* 3.7 29.7 - - - +
127A TYR* 3.3 12.0 - - - +
128A SER* 3.0 39.2 + - - +
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Residues in contact with MET 120 (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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43A PHE* 4.0 29.6 - - + -
45A HIS* 4.2 18.6 - - + -
47A ILE* 4.1 24.9 - - + -
56A VAL* 4.4 9.6 - - + -
57A HIS 3.3 6.7 - - - +
118A PHE* 4.0 8.4 - - + -
119A ARG* 1.3 74.2 - - - +
121A GLU* 1.3 66.7 + - - +
122A ARG* 4.2 15.3 - - + -
125A THR* 4.1 17.3 - - - +
126A LYS* 3.4 1.0 - - - -
127A TYR* 2.9 43.8 + - + +
129A TYR* 4.1 21.1 - - + +
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Residues in contact with GLU 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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55A PRO 3.5 2.8 - - - +
56A VAL* 3.6 0.5 - - - -
57A HIS* 2.8 51.8 + - + +
59A TYR* 2.9 35.4 + - + -
77A LYS* 5.2 1.7 - - - +
119A ARG* 2.8 31.7 + - - +
120A MET* 1.3 82.1 - - - +
122A ARG* 1.3 61.4 + - - +
123A GLY 4.1 1.6 - - - +
125A THR 3.4 4.5 - - - -
126A LYS* 3.8 32.5 + - + +
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Residues in contact with ARG 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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47A ILE* 3.7 40.7 - - + +
51A ASP* 3.2 32.4 + - + +
52A LYS* 2.7 28.3 + - - +
54A SER* 3.6 18.5 + - - +
55A PRO 3.7 5.8 - - - +
56A VAL* 3.7 26.0 - - + +
97A SER 5.5 3.2 + - - -
120A MET* 4.2 13.9 - - + -
121A GLU* 1.3 74.8 - - - +
123A GLY* 1.3 65.4 + - - +
124A SER 3.2 0.3 + - - -
125A THR* 2.7 26.8 + - - +
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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