Contacts of the helix formed by residues 128 - 137 (chain A) in PDB entry 2H35
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 PHE 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A LEU* 3.4 22.0 - - + -
6A ASP 4.7 6.1 - - - +
7A LYS* 5.0 6.1 - - + -
10A VAL* 3.6 31.2 - - + -
11A LYS* 5.0 4.5 - - - -
66A LEU* 3.8 23.3 - - + -
69A ALA* 4.5 15.9 - - + -
70A VAL* 4.5 13.2 - - + -
73A VAL* 4.1 22.2 - - + -
76A MET* 4.7 0.4 - - + -
124A SER* 2.6 26.7 + - - +
125A LEU* 4.5 4.0 - - + -
127A LYS* 1.3 83.0 - - + +
129A LEU* 1.3 58.9 + - + +
130A ALA 2.9 0.8 + - - -
131A SER* 2.9 24.7 + - - -
132A VAL* 3.4 26.3 - - + +
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Residues in contact with LEU 129 (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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66A LEU* 5.0 11.0 - - + -
98A PHE* 4.0 13.9 - - + -
101A LEU* 5.7 1.3 - - + -
102A SER* 4.0 35.7 - - - +
105A LEU* 5.3 9.0 - - + -
125A LEU* 3.1 32.1 + - + +
126A ASP* 3.7 14.4 - - - +
127A LYS 2.6 3.4 + - - -
128A PHE* 1.3 74.4 - - + +
130A ALA* 1.3 57.4 + - - +
131A SER 3.1 0.2 - - - -
132A VAL* 3.4 12.8 - - + -
133A SER* 2.4 41.1 + - - -
142A HEM 3.6 31.6 - - + -
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Residues in contact with ALA 130 (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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2A LEU* 5.0 6.7 - - + -
126A ASP 4.6 0.8 + - - -
127A LYS* 2.4 42.6 + - + +
129A LEU* 1.3 67.8 - - - +
131A SER* 1.3 53.9 + - - +
133A SER* 4.4 4.9 - - - -
134A THR* 2.4 38.0 + - - +
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Residues in contact with SER 131 (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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1A VAL* 3.7 19.3 - - - -
2A LEU* 3.4 28.2 - - - +
76A MET* 3.0 27.0 - - - +
128A PHE* 2.9 23.4 + - - -
130A ALA* 1.3 79.8 - - - +
132A VAL* 1.3 58.6 + - - +
133A SER 3.4 0.2 - - - -
134A THR* 4.3 3.1 - - - -
135A VAL* 3.0 33.5 + - - +
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Residues in contact with VAL 132 (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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65A ALA* 5.2 3.8 - - + -
66A LEU* 4.3 8.5 - - + +
69A ALA* 5.2 2.9 - - + -
76A MET* 4.6 6.1 - - + -
80A LEU* 4.9 8.3 - - + -
128A PHE* 3.4 39.9 - - + +
129A LEU* 2.8 18.3 + - + +
131A SER* 1.3 81.3 - - - +
133A SER* 1.3 60.8 + - - +
135A VAL* 3.1 22.3 - - + +
136A LEU* 3.2 24.2 - - + +
142A HEM 3.5 36.3 - - + -
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Residues in contact with SER 133 (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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98A PHE* 2.9 43.9 - - - -
129A LEU 2.4 31.8 + - - -
130A ALA* 4.2 5.2 - - - -
132A VAL* 1.3 69.5 - - - +
134A THR* 1.3 63.8 + - - +
136A LEU* 3.3 7.9 + - - +
137A THR* 3.2 22.9 + - - +
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Residues in contact with THR 134 (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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1A VAL* 6.0 7.0 - - + -
130A ALA* 2.4 27.6 + - - +
131A SER* 4.3 5.2 - - - -
133A SER* 1.3 79.8 - - - +
135A VAL* 1.3 60.2 + - + +
137A THR* 3.3 6.8 + - + -
138A SER* 2.8 35.5 + - - +
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Residues in contact with VAL 135 (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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1A VAL* 5.7 4.0 - - + -
76A MET* 4.3 7.2 - - + -
77A PRO* 3.6 44.1 - - + +
80A LEU* 3.8 34.3 - - + +
81A SER* 4.8 1.6 - - - -
84A SER* 3.3 14.9 - - - -
131A SER 3.0 23.1 + - - +
132A VAL* 3.1 20.4 - - - +
134A THR* 1.3 80.1 - - + +
136A LEU* 1.3 64.5 + - + +
137A THR 3.3 0.2 + - - -
138A SER* 3.3 14.1 + - - +
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Residues in contact with LEU 136 (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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80A LEU 5.3 0.4 - - - +
83A LEU* 4.0 36.1 - - + -
84A SER* 3.1 24.7 + - - +
87A HIS* 5.0 18.9 - - + +
88A ALA* 5.2 1.9 - - - +
98A PHE* 4.2 12.3 - - + -
132A VAL* 3.2 31.2 + - + +
133A SER* 3.6 8.1 - - - +
134A THR 3.2 1.0 - - - -
135A VAL* 1.3 89.5 - - + +
137A THR* 1.3 60.0 + - - +
142A HEM 4.0 42.4 - - + +
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Residues in contact with THR 137 (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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84A SER* 3.9 3.8 - - - -
88A ALA* 5.7 6.3 - - - +
95A PRO* 5.7 7.2 - - - +
133A SER* 3.2 19.1 - - - +
134A THR* 3.3 6.2 + - + +
135A VAL 3.1 0.2 - - - -
136A LEU* 1.3 82.8 - - - +
138A SER* 1.3 68.2 + - - +
139A LYS* 3.1 6.1 + - - +
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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