Contacts of the strand formed by residues 127 - 134 (chain H) in PDB entry 1H4O
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 ARG 127 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H GLY 3.4 6.1 - - - +
40H PRO* 3.8 10.9 - - + +
46H GLY* 4.4 0.6 - - - -
47H CYS* 3.3 23.2 - - - +
51H HIS* 3.1 51.5 + - + +
125H LEU 3.7 1.6 + - - -
126H LYS* 1.3 72.1 - - - +
128H PHE* 1.3 59.2 + - - +
142H VAL* 3.9 2.9 - - - +
143H GLU* 3.1 31.2 + - + +
146H GLY 2.9 18.0 + - - +
147H THR 2.9 18.4 + - - -
148H GLY 2.8 26.7 + - - -
149H LEU* 3.5 18.8 - - - +
152H SER* 3.1 16.8 - - - +
1162H BEZ 2.8 34.8 + - - -
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Residues in contact with PHE 128 (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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36H LEU* 3.8 24.5 - - + -
37H PHE* 3.2 9.9 - - - +
38H GLY* 2.8 49.7 + - - +
51H HIS* 4.0 2.4 - - - -
73H LEU* 4.8 2.5 - - + -
104H PHE* 3.7 28.9 - + - -
110H LEU* 4.3 15.9 - - + -
125H LEU* 4.3 11.9 - - + -
126H LYS 3.4 14.8 - - - +
127H ARG* 1.3 75.6 - - - +
129H SER* 1.3 70.0 + - - +
130H MET* 3.9 26.7 - - + -
140H LEU* 4.5 1.3 - - + -
141H ASN 3.0 14.4 - - - +
142H VAL* 4.1 16.4 - - + -
152H SER* 3.8 7.2 - - - -
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Residues in contact with SER 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H VAL* 5.3 0.4 - - - -
36H LEU 3.3 8.1 - - - -
37H PHE* 3.9 10.1 - - - -
55H PHE* 4.5 0.7 - - - -
128H PHE* 1.3 74.3 - - - +
130H MET* 1.3 65.3 + - - +
140H LEU* 3.6 2.4 - - - +
141H ASN* 2.7 60.7 + - - +
151H CYS 3.9 0.2 + - - -
152H SER* 3.5 24.1 + - - -
157H ILE* 3.4 18.8 - - - +
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Residues in contact with MET 130 (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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3H ILE* 4.0 33.7 - - + -
9H ILE* 3.7 24.2 - - + -
35H VAL* 3.3 9.7 - - - +
36H LEU* 2.8 43.2 + - + +
104H PHE* 4.2 4.7 - - + -
110H LEU* 4.2 6.1 - - + -
128H PHE* 3.9 15.9 - - + -
129H SER* 1.3 80.0 - - - +
131H VAL* 1.3 59.1 + - - +
132H VAL* 4.0 10.5 - - + -
137H VAL* 3.9 12.3 - - + -
139H ALA 3.1 11.9 - - - +
140H LEU* 3.8 24.7 - - + -
157H ILE* 3.8 6.3 - - - -
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Residues in contact with VAL 131 (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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33H LYS* 4.7 7.4 - - + -
34H GLY 3.5 7.6 - - - +
35H VAL* 4.7 1.1 - - + +
130H MET* 1.3 73.4 - - - +
132H VAL* 1.3 66.7 + - - +
133H GLN* 5.6 1.6 - - + +
137H VAL* 3.7 4.0 - - - +
138H LYS* 2.8 38.6 + - + -
139H ALA* 3.0 28.2 + - + +
157H ILE* 3.6 22.4 - - + +
160H GLN* 4.5 13.5 - - + +
161H LEU* 3.9 35.4 - - + -
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Residues in contact with VAL 132 (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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9H ILE* 3.9 23.1 - - + -
29H PHE* 3.9 30.0 - - + -
32H LYS 3.7 1.1 - - - +
33H LYS* 3.5 3.3 - - - +
34H GLY 2.8 40.1 + - - +
36H LEU* 4.5 5.2 - - + -
130H MET* 4.0 22.4 - - + +
131H VAL* 1.3 80.4 - - - +
133H GLN* 1.3 62.7 + - - +
134H ASP 4.1 0.2 - - - -
135H GLY* 3.5 35.4 - - - +
136H ILE 3.4 5.2 - - - +
137H VAL* 4.9 2.0 - - - -
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Residues in contact with GLN 133 (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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145G ASP* 4.9 5.5 + - - -
31H GLY 5.5 0.8 - - - -
32H LYS* 3.6 6.6 + - - +
33H LYS* 3.0 57.2 - - - +
131H VAL* 4.3 2.6 - - + +
132H VAL* 1.3 72.7 - - - +
134H ASP* 1.3 80.6 + - + +
136H ILE* 2.8 26.7 + - - +
138H LYS* 3.9 27.1 - - + +
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Residues in contact with ASP 134 (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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29H PHE 3.5 11.2 - - - -
30H LYS* 4.2 8.9 + - - +
31H GLY* 3.3 25.7 + - - +
32H LYS 2.8 16.7 + - - +
132H VAL 4.1 0.2 - - - -
133H GLN* 1.3 81.5 - - + +
135H GLY* 1.3 55.3 + - - +
136H ILE* 3.3 11.0 + - + +
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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