Contacts of the strand formed by residues 215 - 220 (chain A) in PDB entry 4H2G
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 ILE 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY* 3.3 6.3 - - - +
174A VAL* 4.4 7.0 - - + -
204A VAL* 4.2 23.8 - - + -
207A LEU* 3.9 30.1 - - + -
208A LYS* 3.9 20.0 - - + +
212A VAL* 3.7 20.4 - - + +
214A LYS* 1.3 83.4 - - - +
216A ILE* 1.4 73.2 - - - +
235A GLY 3.4 24.5 - - - +
236A VAL* 4.2 7.9 - - + -
237A ASP* 2.8 42.8 + - - +
238A VAL 3.4 1.4 + - - +
294A PHE* 5.3 0.6 - - - -
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Residues in contact with ILE 216 (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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29A LEU* 4.2 6.5 - - + -
31A ILE* 3.9 25.8 - - + -
79A LEU* 4.0 17.7 - - + -
81A LEU* 4.2 16.6 - - + -
171A VAL* 3.7 24.0 - - + -
172A GLY 2.8 12.4 + - - +
173A ILE* 3.3 8.8 - - + -
174A VAL 2.9 25.5 + - - -
215A ILE* 1.4 79.5 - - - +
217A ALA* 1.4 73.0 + - - +
218A LEU* 3.8 4.4 + - + +
238A VAL* 3.5 15.3 - - + +
240A VAL* 3.9 21.3 - - + -
294A PHE* 5.9 3.8 - - + -
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Residues in contact with ALA 217 (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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174A VAL* 3.4 9.4 - - + +
176A TYR* 3.9 18.8 - - + -
200A LEU* 5.1 5.4 - - + -
215A ILE* 4.1 1.0 - - - -
216A ILE* 1.4 72.5 - - - +
218A LEU* 1.3 55.0 + - - +
229A ILE* 4.1 14.8 - - + -
236A VAL* 3.9 27.8 - - + +
238A VAL 2.9 8.0 + - - +
239A VAL* 3.3 6.4 - - + +
240A VAL 2.8 31.9 + - - +
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Residues in contact with LEU 218 (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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81A LEU* 4.0 18.2 - - + -
82A ASP 3.5 27.4 - - - +
83A ALA* 3.9 7.6 - - + -
112A ALA* 4.1 13.7 - - + +
113A MET 4.0 6.7 - - - +
114A ALA* 3.4 19.2 - - + +
140A LEU* 4.7 2.2 - - + -
173A ILE* 3.6 29.4 - - + -
174A VAL 2.8 8.8 + - - +
175A GLY* 3.1 24.8 - - - -
176A TYR* 3.3 2.3 + - - -
216A ILE* 3.8 4.4 + - + -
217A ALA* 1.3 73.6 - - - +
219A GLY* 1.3 58.8 + - - +
240A VAL* 3.4 35.2 - - + +
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Residues in contact with GLY 219 (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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83A ALA* 3.6 6.5 - - - +
114A ALA* 3.7 5.8 - - - -
176A TYR* 3.1 34.3 - - - -
218A LEU* 1.3 78.2 - - - +
220A HIS* 1.3 59.7 + - - -
221A SER 4.1 0.2 + - - -
240A VAL 3.0 8.3 + - - +
241A GLY* 3.2 26.2 - - - -
242A GLY 3.4 2.8 + - - -
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Residues in contact with HIS 220 (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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36A ASP* 3.2 17.0 + - - -
83A ALA 2.7 24.6 + - - +
84A GLY 3.7 2.9 - - - -
85A ASP* 3.1 22.6 + - + -
115A LEU 3.5 21.1 - - - +
116A GLY* 3.3 13.0 - - - -
117A ASN* 3.0 10.9 + - + -
176A TYR* 2.9 9.0 + - - +
178A SER* 2.8 26.2 + - - -
219A GLY* 1.3 72.8 - - - -
221A SER* 1.3 55.4 + - - +
222A GLY 3.8 0.9 - - - -
242A GLY 4.7 1.3 - - - +
243A HIS* 3.1 21.6 + + + +
601A ZN 2.0 36.8 - - - -
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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