Contacts of the strand formed by residues 198 - 208 (chain A) in PDB entry 2HVY
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 ALA 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A MET* 3.7 26.0 - - + -
118A HIS 3.3 14.1 - - - +
119A LEU* 3.8 8.1 - - + -
120A HIS* 3.6 11.0 + - - -
187A ILE* 3.9 4.9 - - - +
188A HIS* 3.9 24.0 + - - +
191A GLY* 3.6 19.0 - - - -
197A GLY* 1.3 76.7 - - - +
199A HIS* 1.3 62.2 + - - +
13B GLN* 4.8 3.3 + - - -
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Residues in contact with HIS 199 (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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117A MET* 3.5 2.4 - - - -
118A HIS* 2.9 46.5 + - + -
120A HIS* 2.9 24.9 + - + +
184A ARG* 4.3 12.1 - - - +
187A ILE* 3.5 7.9 - - - -
188A HIS* 5.5 1.1 - - - +
198A ALA* 1.3 75.2 - - - +
200A MET* 1.3 77.9 + - - +
201A SER* 3.5 15.8 + - - -
501A ATP 3.2 38.7 - + - -
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Residues in contact with MET 200 (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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87A LYS* 5.8 0.3 + - - -
88A VAL* 5.1 4.9 - - + -
115A ALA* 4.9 0.7 - - + -
116A LEU 3.6 4.5 - - - +
182A TYR* 6.4 0.4 - - + -
183A ILE* 3.9 11.2 - - - -
184A ARG* 3.0 94.4 + - + +
187A ILE* 3.6 21.4 - - + +
199A HIS* 1.3 73.5 - - - +
201A SER* 1.3 60.0 + - - +
202A GLU* 3.9 16.4 - - - +
203A LEU* 3.8 39.3 - - + +
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Residues in contact with SER 201 (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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87A LYS* 5.1 10.1 + - - -
116A LEU* 3.0 35.2 + - - +
118A HIS* 4.6 11.1 - - - +
170A ASP* 5.0 0.9 + - - -
184A ARG* 5.7 0.9 - - - -
199A HIS* 3.5 20.9 + - - -
200A MET* 1.3 73.7 - - - +
202A GLU* 1.3 65.8 + - - +
4C ARG* 5.7 1.0 - - - -
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Residues in contact with GLU 202 (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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115A ALA* 3.5 2.9 - - - -
116A LEU* 2.9 34.9 + - + +
200A MET* 3.5 8.1 - - - +
201A SER* 1.3 83.7 + - - +
203A LEU* 1.3 65.0 + - - +
3C PHE* 3.3 33.0 - - + +
4C ARG* 2.8 33.4 + - - +
5C ILE* 3.0 47.8 + - + +
30C ALA* 5.7 0.5 - - - +
31C HIS* 5.4 1.4 + - - +
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Residues in contact with LEU 203 (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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85A ASP* 6.1 0.7 - - - +
87A LYS 4.5 4.1 + - - +
88A VAL* 3.5 31.4 - - + +
89A SER* 3.5 18.0 + - - -
113A TYR* 3.7 39.5 - - + -
114A VAL 3.8 2.2 - - - +
115A ALA* 3.6 26.9 - - + -
183A ILE* 3.8 20.0 - - + -
200A MET* 3.8 30.3 - - + +
202A GLU* 1.3 79.9 - - - +
204A ARG* 1.3 64.6 + - - +
5C ILE* 5.1 1.8 - - - -
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Residues in contact with ARG 204 (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 ASP* 2.9 42.2 + - - -
89A SER* 3.0 31.2 + - - +
90A GLY* 3.5 6.6 - - - +
113A TYR* 3.3 6.2 - - - -
114A VAL* 2.8 43.8 + - + +
203A LEU* 1.3 76.6 - - - +
205A ARG* 1.3 69.0 + - - +
206A THR* 3.6 2.4 + - + -
213A GLU* 2.7 23.2 + - - +
217A LEU* 3.9 5.3 - - - +
5C ILE* 5.2 7.2 - - + -
7C LYS* 5.8 0.6 - - - +
14C TYR* 2.9 27.9 + - - +
30C ALA* 3.2 39.9 + - - +
32C PRO* 3.7 3.4 - - - +
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Residues in contact with ARG 205 (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 GLY 3.7 3.0 + - - -
82A GLY 3.0 37.4 + - - -
83A THR 3.6 10.7 + - - -
84A LEU* 3.5 32.3 - - + +
88A VAL* 4.3 1.2 - - - +
89A SER 2.9 10.0 + - - +
90A GLY* 3.2 5.7 - - - -
91A VAL* 3.0 50.5 + - - +
92A LEU* 4.3 3.0 - - - +
93A PRO* 4.4 0.4 - - - +
111A LYS* 3.6 22.8 - - - +
112A GLU 3.4 10.1 - - - +
113A TYR* 3.7 22.7 + - + -
204A ARG* 1.3 75.4 + - - +
206A THR* 1.3 59.2 + - - +
207A ARG 3.4 25.8 - - - +
208A SER* 3.7 21.7 + - - -
213A GLU* 5.0 0.5 - - - +
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Residues in contact with THR 206 (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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91A VAL* 3.6 7.6 - - - -
112A GLU* 2.7 43.4 + - - +
113A TYR* 3.8 2.3 + - - -
114A VAL* 3.6 28.0 - - + -
174A ARG* 3.8 5.1 + - - +
204A ARG* 4.1 7.6 - - + +
205A ARG* 1.3 76.1 - - - +
207A ARG* 1.3 61.1 + - - +
212A LYS* 3.5 3.3 - - - +
213A GLU* 3.3 51.7 + - - +
14C TYR* 3.8 9.4 - - + +
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Residues in contact with ARG 207 (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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11A ARG 5.6 0.8 + - - -
13A LEU* 4.1 23.7 - - + +
15A ALA* 4.1 12.3 + - - +
16A ASP* 2.6 45.8 + - - -
91A VAL* 3.9 1.8 - - - +
111A LYS* 3.5 4.0 - - - -
112A GLU* 3.1 46.7 + - + +
160A TYR* 5.4 3.8 + - - -
205A ARG* 3.4 14.9 - - - +
206A THR* 1.3 81.7 - - - +
208A SER* 1.3 60.7 + - - +
209A GLY 3.0 24.1 + - - +
210A PRO* 4.8 7.3 + - - +
211A PHE 3.3 16.4 - - - +
212A LYS* 4.2 21.7 - - + +
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Residues in contact with SER 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLY 3.1 23.4 + - - -
91A VAL* 3.9 13.8 - - - +
93A PRO* 4.0 7.8 - - - +
106A LEU* 4.5 6.7 + - - +
109A ALA* 5.0 0.7 - - - -
111A LYS* 3.7 17.2 - - - -
205A ARG* 3.7 20.9 + - - -
207A ARG* 1.3 73.4 - - - +
209A GLY* 1.3 63.8 + - - +
210A PRO* 3.4 4.0 - - - +
211A PHE* 2.9 28.0 + - - +
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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