Contacts of the strand formed by residues 48 - 54 (chain H) in PDB entry 1YI2
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 VAL 48 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46H TYR* 4.1 2.8 - - - +
47H PRO* 1.3 80.3 - - - +
49H GLN* 1.3 63.8 + - - +
50H ILE* 3.7 30.7 - - + -
140H TYR* 3.4 5.7 - - - +
141H CYS* 2.9 49.4 + - - +
143H VAL* 3.7 39.7 - - + +
146H ALA* 4.5 9.0 - - + -
168H VAL* 4.5 8.1 - - + -
170H ARG 3.0 6.1 - - - +
171H GLY* 4.7 4.3 - - - -
173H GLU* 3.9 7.2 - - - +
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Residues in contact with GLN 49 (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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46H TYR 6.1 0.4 - - - +
48H VAL* 1.3 76.0 - - - +
50H ILE* 1.3 60.6 + - - +
51H SER* 4.5 2.3 + - - +
91H ARG* 5.7 1.0 - - - +
135H GLN* 5.2 1.9 - - - +
138H THR* 3.9 11.8 - - + +
139H ALA 3.5 5.4 - - - +
140H TYR* 2.9 44.1 + - + -
168H VAL* 3.6 0.5 - - - +
169H GLU* 2.7 62.0 + - - +
170H ARG* 3.2 27.9 + - + +
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Residues in contact with ILE 50 (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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48H VAL* 3.7 20.8 - - + -
49H GLN* 1.3 79.3 - - - +
51H SER* 1.3 62.0 + - - +
138H THR* 4.7 0.2 - - - -
139H ALA* 2.7 38.7 + - - +
141H CYS* 5.6 0.4 - - - -
146H ALA* 4.2 4.3 - - + +
149H VAL* 3.4 33.9 - - + -
150H LYS* 4.0 13.5 - - + -
153H PHE* 3.1 17.8 - - + -
166H ILE* 3.7 27.6 - - + -
167H LYS 3.3 13.0 - - - +
168H VAL* 3.6 24.9 - - + -
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Residues in contact with SER 51 (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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49H GLN* 4.3 7.0 + - - -
50H ILE* 1.3 74.7 - - - +
52H LEU* 1.3 63.0 + - - +
53H ILE* 3.8 8.0 + - - -
135H GLN* 2.8 27.0 + - - -
137H PHE 3.0 12.8 - - - -
138H THR* 2.6 25.7 + - - +
153H PHE* 3.7 4.0 - - - -
166H ILE* 3.8 2.4 - - - -
167H LYS* 2.9 34.9 + - - +
169H GLU* 4.6 5.7 - - - +
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Residues in contact with LEU 52 (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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51H SER* 1.3 72.7 - - - +
53H ILE* 1.3 59.4 + - - +
54H VAL* 6.0 0.2 - - + -
135H GLN* 3.5 2.6 - - - -
136H LEU* 2.9 31.7 + - + +
137H PHE* 2.7 44.1 + - + +
153H PHE* 3.7 15.5 - - + +
156H ALA* 4.4 6.1 - - + -
157H TYR* 4.1 31.6 - - + +
160H ILE* 4.4 15.0 - - + -
164H CYS* 3.5 26.7 - - + -
165H ARG 3.6 7.9 - - - +
166H ILE* 4.1 18.4 - - + -
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Residues in contact with ILE 53 (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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51H SER* 4.4 7.9 - - - +
52H LEU* 1.3 76.2 - - - +
54H VAL* 1.3 60.9 + - - +
55H GLU* 3.5 1.2 + - - +
133H GLY* 3.2 33.0 - - - +
134H GLU 3.1 19.7 - - - +
135H GLN* 4.6 9.0 - - + +
164H CYS* 3.1 8.5 - - - +
165H ARG* 2.8 64.3 + - + +
167H LYS* 3.5 44.6 - - + +
169H GLU* 4.9 3.6 - - - +
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Residues in contact with VAL 54 (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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52H LEU* 4.0 0.8 + - + -
53H ILE* 1.3 72.5 - - - +
55H GLU* 1.3 55.2 + - - +
56H GLU 2.8 32.5 - - - +
58H VAL* 4.4 2.9 - - + -
60H LEU* 4.8 2.9 - - + -
130H VAL* 3.9 32.1 - - + -
131H GLN 4.5 2.0 - - - +
133H GLY* 2.6 36.2 + - - -
134H GLU 3.1 7.5 + - - +
136H LEU* 4.3 26.5 - - + -
160H ILE* 4.5 1.1 - - + -
162H PRO* 3.8 24.2 - - + -
163H SER 4.1 3.6 - - - -
164H CYS* 4.3 8.1 - - - -
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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