Contacts of the strand formed by residues 107 - 112 (chain H) in PDB entry 2VUU
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 HIS 107 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75H HIS 3.4 2.4 + - - -
76H LEU* 3.5 19.8 - - + -
77H ALA 3.1 23.0 + - - -
105H ILE* 3.6 2.7 - - - +
106H GLN* 1.3 81.5 - - + +
108H TYR* 1.3 63.6 + - - +
109H ILE* 3.9 8.4 - - + +
144H PRO 3.4 6.1 - - - -
145H SER 4.5 3.4 - - - -
146H THR* 3.1 27.9 + - - -
203H ILE* 3.3 36.3 + - + -
204H PHE* 3.5 23.1 + + + -
207H GLY* 3.5 20.6 - - - -
208H PRO* 3.6 24.8 - - + +
211H TRP* 4.6 0.9 - - + -
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Residues in contact with TYR 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H PHE* 4.2 7.6 - + - -
77H ALA* 3.8 13.9 - - + -
79H ILE* 3.4 33.7 - - + +
92H GLY 4.6 1.7 + - - -
95H LEU* 3.7 8.0 - - - +
96H ALA* 3.6 23.8 + - - +
99H ALA* 3.6 32.5 - - + -
105H ILE* 3.8 12.5 - - + +
107H HIS* 1.3 73.7 - - - +
109H ILE* 1.3 62.4 + - - +
110H TYR* 3.7 16.2 + + + -
134H VAL* 6.1 0.3 - - - +
138H VAL* 4.1 31.8 - - + +
143H LEU* 4.2 14.1 - - + -
144H PRO 2.7 14.6 + - - +
145H SER* 2.9 35.2 - - - -
146H THR 3.3 0.7 + - - +
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Residues in contact with ILE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77H ALA 2.8 13.5 + - - +
78H PHE* 3.3 12.6 - - + -
79H ILE* 2.8 27.0 + - - +
107H HIS* 3.9 12.8 + - + +
108H TYR* 1.3 75.0 - - - +
110H TYR* 1.3 62.1 + - - +
146H THR* 3.2 16.6 - - - +
148H VAL* 3.7 30.7 - - + -
200H LEU* 4.0 11.7 - - + +
203H ILE* 3.4 32.8 - - + -
204H PHE* 3.3 38.1 - - + -
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Residues in contact with TYR 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79H ILE* 3.4 35.0 - - + -
81H THR* 4.6 19.2 + - + +
88H GLU* 4.9 1.7 + - - +
92H GLY* 5.1 1.1 - - - -
108H TYR* 3.7 18.5 + + + -
109H ILE* 1.3 73.0 - - - +
111H SER* 1.3 79.3 + - - +
112H SER* 3.3 11.4 + - - -
131H LYS* 3.6 35.3 - - + +
134H VAL* 3.5 38.0 - - + +
135H GLU* 4.4 3.8 - - - -
138H VAL* 4.6 1.3 - - + -
146H THR 3.1 6.5 + - - -
147H PHE* 3.3 35.0 - + + -
148H VAL* 3.2 21.8 + - - -
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Residues in contact with SER 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17H GLN* 2.8 31.7 + - - -
78H PHE* 4.2 8.2 - - - -
79H ILE 2.7 10.6 + - - +
80H ASN* 3.5 26.8 + - - +
81H THR 5.4 0.5 + - - -
109H ILE 4.2 0.2 + - - -
110H TYR* 1.3 87.2 - - - +
112H SER* 1.3 59.9 + - - +
131H LYS* 4.0 12.4 + - - +
148H VAL* 3.5 18.3 + - - +
150H ALA* 4.9 5.4 + - - +
218H LEU* 5.7 0.3 - - - +
1353H NAP 5.9 1.0 - - - -
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Residues in contact with SER 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H TYR* 3.3 17.1 + - - -
111H SER* 1.3 75.5 + - - +
113H MET* 1.3 91.0 + - - +
131H LYS* 4.2 2.2 - - - -
132H PHE* 3.9 11.4 + - - -
135H GLU* 2.6 30.1 + - - +
147H PHE* 4.3 4.7 - - - -
148H VAL 2.9 16.5 + - - +
149H TYR* 3.5 24.3 + - - -
150H ALA 4.4 0.9 + - - -
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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