Contacts of the strand formed by residues 122 - 130 (chain H) in PDB entry 1YHQ
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 LYS 122 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H ARG* 3.2 2.9 - - - -
100H GLU 2.9 31.0 + - - +
102H LYS* 3.4 42.7 - - + +
120H PHE 3.9 0.2 + - - -
121H GLY* 1.3 74.2 - - - -
123H ILE* 1.3 72.6 + - - +
124H VAL* 3.5 5.7 + - + +
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Residues in contact with ILE 123 (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 TYR* 4.8 10.1 - - + +
23H ILE* 3.1 31.2 - - + -
24H THR* 2.8 30.1 - - - +
25H GLY 3.7 12.7 - - - +
26H ILE* 3.9 5.6 - - + -
27H PRO* 3.6 25.7 - - + +
97H VAL* 3.8 23.6 - - + -
98H LEU 3.6 4.3 - - - +
99H ARG* 4.6 1.8 - - + +
120H PHE* 6.5 0.7 - - + -
121H GLY 5.2 2.5 - - - +
122H LYS* 1.3 85.9 - - - +
124H VAL* 1.3 65.8 + - - +
125H GLY 4.3 1.1 - - - +
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Residues in contact with VAL 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H TYR* 3.5 27.4 - - + +
27H PRO* 3.7 14.7 - - - +
62H HIS* 5.3 1.7 - - - -
98H LEU* 2.9 21.8 + - + +
99H ARG 3.6 8.5 - - - +
100H GLU* 3.7 21.8 - - + +
102H LYS* 4.0 20.2 - - - +
122H LYS* 3.7 12.6 - - + +
123H ILE* 1.3 80.3 - - - +
125H GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 125 (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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26H ILE* 4.5 1.6 - - - +
27H PRO* 3.9 13.9 - - - +
62H HIS* 4.4 10.8 - - - -
97H VAL* 3.5 5.7 - - - +
98H LEU* 2.8 39.8 + - - +
124H VAL* 1.3 80.7 - - - +
126H THR* 1.3 67.1 + - - +
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Residues in contact with THR 126 (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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20H ARG* 4.1 10.1 - - - +
26H ILE* 3.6 26.0 - - + -
27H PRO 4.4 8.8 + - - +
29H SER* 4.9 3.6 - - - -
61H ARG* 3.5 2.8 - - - +
62H HIS* 3.0 47.4 + - - +
94H PRO* 3.6 27.4 - - - +
96H GLN 3.1 9.6 - - - +
97H VAL* 4.5 4.3 - - + -
98H LEU* 3.9 6.1 - - - +
125H GLY* 1.3 81.4 - - - +
127H ALA* 1.3 61.5 + - - +
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Residues in contact with ALA 127 (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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59H GLN* 4.3 11.7 - - + -
60H LEU 3.2 26.0 - - - +
61H ARG* 3.8 5.4 - - + -
94H PRO* 3.4 8.1 - - - -
95H HIS 3.1 4.0 + - - -
96H GLN* 2.7 38.3 + - + +
98H LEU* 3.9 21.3 - - + -
126H THR* 1.3 77.3 - - - +
128H ALA* 1.3 59.9 - - - +
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Residues in contact with ALA 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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59H GLN* 3.2 3.4 - - - -
60H LEU* 2.8 37.5 + - + +
65H LEU* 4.9 10.1 - - + -
92H LYS* 4.2 20.0 - - + -
93H PHE 3.6 25.6 - - - +
94H PRO* 3.7 5.3 - - + +
95H HIS 4.5 0.4 - - - +
127H ALA* 1.3 74.8 - - - +
129H ARG* 1.3 64.0 + - - +
130H VAL* 3.7 7.1 + - + +
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Residues in contact with ARG 129 (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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10040 C 4.3 14.0 + - - -
10050 A 5.6 4.7 + - - -
12H ILE* 3.7 39.1 - - + +
14H LYS* 2.6 32.5 + - - +
15H PRO 3.5 0.2 + - - -
16H ALA* 3.8 22.2 - - - +
58H VAL 3.4 4.0 - - - -
59H GLN* 2.7 30.1 - - + +
92H LYS* 4.7 3.6 - - - +
96H GLN* 3.0 37.1 - - + +
127H ALA 4.1 0.6 + - - -
128H ALA* 1.3 73.3 - - - +
130H VAL* 1.3 62.0 + - - +
131H GLN* 4.2 7.2 + - - +
134H GLU* 4.3 2.1 - - - +
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Residues in contact with VAL 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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54H VAL* 3.9 26.5 - - + -
56H GLU 3.9 0.7 - - - +
57H THR* 3.2 5.3 - - - +
58H VAL* 2.8 45.3 + - + +
60H LEU* 4.2 19.1 - - + -
92H LYS* 4.1 24.0 - - + -
128H ALA* 4.2 11.2 - - + +
129H ARG* 1.3 79.3 - - - +
131H GLN* 1.3 73.6 + - - +
134H GLU* 3.6 18.6 - - + +
136H LEU* 4.3 9.0 - - + -
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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