Contacts of the strand formed by residues 114 - 122 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ARG* 4.3 7.0 - - - -
112B ASP 3.4 1.0 + - - -
113B ASN* 1.3 81.9 - - - +
115B SER* 1.3 60.8 + - - -
116B TYR* 3.6 9.5 - - - -
135B SER* 3.6 2.0 - - - -
136B VAL 2.8 34.3 + - - -
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Residues in contact with SER 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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62B ARG* 3.7 4.9 - - - +
63B GLU* 2.8 49.6 + - - +
114B GLY* 1.3 72.1 - - - -
116B TYR* 1.3 67.2 + - - +
133B GLN* 3.6 14.7 - - - +
134B LEU 3.2 7.2 - - - -
135B SER* 3.2 20.8 + - - -
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Residues in contact with TYR 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 TRP* 3.9 19.8 - - + -
61B PHE 3.1 18.8 - - - +
62B ARG* 3.3 36.8 + - + -
63B GLU 4.3 0.7 - - - +
73B VAL* 4.0 18.8 - - + -
86B THR* 5.5 2.0 - - + +
90B PHE* 3.8 25.6 - + - -
103B LEU* 5.5 3.1 - - + -
112B ASP* 2.5 35.7 + - - -
114B GLY 3.6 18.8 - - - -
115B SER* 1.3 75.3 - - - +
117B PHE* 1.3 60.9 + - - +
133B GLN* 3.4 7.8 - - - +
134B LEU* 2.7 45.0 + - + +
136B VAL* 3.7 18.8 - - + -
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B TYR 3.9 0.2 - - - +
60B TRP* 3.4 9.0 - - - -
61B PHE* 2.9 62.2 + + + -
62B ARG 3.3 26.5 - - - -
63B GLU* 4.1 7.9 - - - -
64B GLY 4.3 2.5 - - - -
65B ALA 3.8 14.6 - - - -
67B ILE* 4.1 5.2 - - + -
116B TYR* 1.3 74.9 - - - +
118B PHE* 1.3 69.0 + - - +
119B ARG* 4.7 0.9 - - + -
128B SER* 4.0 20.9 - - - -
129B TYR 3.4 19.5 - - - +
130B LYS* 3.6 28.0 - - + -
132B PRO 5.5 0.9 - - - -
133B GLN* 3.7 29.6 - - + +
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Residues in contact with PHE 118 (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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23B LEU* 3.6 31.3 - - + +
43B PHE* 3.7 38.8 - + - -
58B GLY* 3.6 14.8 - - - -
59B TYR 3.2 33.7 - - - -
60B TRP* 3.5 35.9 - + + -
92B LEU* 4.2 8.3 - - + -
96B PRO* 4.9 2.5 - - + -
101B CYS* 3.7 19.1 - - + -
117B PHE* 1.3 77.7 - - - +
119B ARG* 1.3 75.3 + - - +
120B MET* 4.2 2.0 - - + -
129B TYR* 2.9 39.5 + + - +
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Residues in contact with ARG 119 (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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58B GLY* 3.3 4.9 - - - -
59B TYR* 2.6 51.4 + - + +
61B PHE* 4.2 12.1 - - + -
67B ILE* 3.6 36.5 - - - +
117B PHE* 4.7 0.7 - - + -
118B PHE* 1.3 81.8 - - - +
120B MET* 1.3 64.9 + - - +
121B GLU* 3.2 28.6 + - - +
126B LYS* 3.7 29.2 - - - +
127B TYR* 3.5 11.7 - - - +
128B SER* 2.8 45.1 + - - +
129B TYR* 4.6 0.2 - - - -
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Residues in contact with MET 120 (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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21B PHE* 4.2 10.1 - - - -
43B PHE* 4.0 19.7 - - + -
45B HIS* 3.8 38.1 - - + +
56B VAL* 4.7 6.3 - - + -
57B HIS 3.4 6.5 - - - +
118B PHE* 4.2 5.6 - - + -
119B ARG* 1.3 76.8 - - - +
121B GLU* 1.3 72.6 + - - +
122B ARG* 3.3 30.7 - - + +
125B THR* 3.2 30.5 - - + +
126B LYS* 3.5 0.3 - - - -
127B TYR* 3.1 36.1 + - + +
129B TYR* 3.8 14.3 - - + +
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Residues in contact with GLU 121 (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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55B PRO 3.4 3.5 - - - +
56B VAL* 3.5 1.4 - - - +
57B HIS* 2.8 51.4 + - + +
59B TYR* 2.9 33.3 + - + -
67B ILE* 4.7 5.0 - - - +
77B LYS* 5.3 1.7 - - - +
119B ARG* 3.2 29.4 + - - +
120B MET* 1.3 82.0 - - - +
122B ARG* 1.3 59.8 + - - +
123B GLY 4.1 1.3 - - - +
125B THR 3.6 4.9 - - - -
126B LYS* 4.0 27.3 + - + +
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Residues in contact with ARG 122 (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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45B HIS* 3.9 15.5 - - - -
46B PRO 5.3 2.2 - - - -
47B ILE* 3.4 39.7 - - - +
48B PRO* 6.2 0.7 - - - -
51B ASP* 3.3 22.2 + - + +
52B LYS* 2.8 35.2 + - - +
54B SER* 3.4 25.3 + - - +
55B PRO 3.6 6.7 - - - +
56B VAL* 3.7 21.6 - - + +
97B SER 5.4 4.2 + - - -
120B MET* 3.3 15.9 - - + +
121B GLU* 1.3 74.1 - - - +
123B GLY* 1.3 60.6 + - - +
124B SER 3.1 0.9 + - - -
125B THR* 2.7 34.1 + - - -
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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