Contacts of the strand formed by residues 135 - 141 (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 GLN 135 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49H GLN* 5.1 4.0 - - - +
51H SER* 2.9 31.9 + - - -
52H LEU 3.5 6.1 - - - -
53H ILE* 4.5 10.3 - - + -
91H ARG* 3.3 47.0 + - - +
92H LYS* 4.4 11.1 - - - -
130H VAL* 5.8 0.2 - - - -
133H GLY 5.2 1.6 - - - +
134H GLU* 1.3 73.5 - - - +
136H LEU* 1.3 60.3 + - - +
138H THR* 3.4 14.7 + - - +
169H GLU* 5.8 2.9 - - - +
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Residues in contact with LEU 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H LEU* 2.9 14.4 + - + +
54H VAL* 4.7 12.8 - - + -
60H LEU* 3.6 27.8 - - + -
65H LEU* 4.1 12.1 - - + -
90H LEU* 3.6 20.1 - - + +
91H ARG* 3.2 28.3 + - - +
92H LYS* 3.9 22.9 - - + -
128H ALA* 6.1 0.2 - - + -
130H VAL* 4.3 7.6 - - + -
134H GLU 3.6 1.8 + - - -
135H GLN* 1.3 73.2 - - - +
137H PHE* 1.3 85.0 + - + +
160H ILE* 3.7 24.0 - - + -
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Residues in contact with PHE 137 (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 MET* 4.6 2.0 - - + -
51H SER* 3.1 5.0 - - - -
52H LEU* 2.8 51.8 + - + +
65H LEU* 4.5 1.6 - - + -
68H SER* 3.6 20.9 - - - -
69H ARG* 3.6 47.1 - - + -
72H ALA* 5.6 1.3 - - + -
88H MET* 4.4 14.6 - - + -
89H THR 3.3 17.5 - - - -
90H LEU* 3.8 22.4 - - + -
91H ARG* 4.8 1.1 - - - -
136H LEU* 1.3 104.0 + - + +
138H THR* 1.3 63.1 + - - +
139H ALA 4.3 0.2 - - - -
153H PHE* 4.0 20.2 - + + -
156H ALA* 4.7 7.6 - - + -
160H ILE* 5.7 0.7 - - + -
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Residues in contact with THR 138 (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* 3.8 12.3 - - + +
50H ILE 3.5 4.3 - - - +
51H SER* 2.6 24.7 + - - +
88H MET* 3.5 1.3 - - - -
89H THR* 2.8 37.8 + - - -
91H ARG* 2.6 31.3 + - - +
135H GLN* 3.4 2.3 + - - +
137H PHE* 1.3 73.7 + - - +
139H ALA* 1.3 60.3 + - - +
140H TYR* 3.2 42.9 - - + +
153H PHE* 4.5 0.7 - - - -
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Residues in contact with ALA 139 (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* 3.4 5.9 - - - +
50H ILE 2.8 31.0 + - - +
76H LEU* 5.1 4.0 - - + -
86H TYR* 5.9 0.7 - - + -
87H LYS 3.3 9.2 - - - +
88H MET* 4.0 14.4 - - + +
138H THR* 1.3 73.4 - - - +
140H TYR* 1.3 68.0 + - - +
141H CYS* 4.3 1.5 - - + -
149H VAL* 3.4 32.3 - - + -
153H PHE* 3.8 9.8 - - + -
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Residues in contact with TYR 140 (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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43H ALA* 3.4 37.8 - - + +
46H TYR* 3.6 18.8 - - + -
48H VAL 3.4 6.5 - - - +
49H GLN* 2.9 48.0 + - + -
86H TYR* 3.3 6.8 - - - +
87H LYS* 2.7 63.8 + - + -
89H THR* 4.4 12.4 - - - -
91H ARG* 4.5 6.8 + - - -
138H THR* 3.2 31.9 - - + +
139H ALA* 1.3 73.7 - - - +
141H CYS* 1.3 62.3 + - - +
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Residues in contact with CYS 141 (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* 3.4 15.0 - - - +
47H PRO* 3.4 6.2 - - - +
48H VAL* 3.0 46.6 + - - +
50H ILE* 5.6 0.7 - - - -
80H LEU* 5.4 0.7 - - + -
85H ASP 4.3 2.2 - - - +
86H TYR* 4.3 10.1 - - + -
139H ALA* 5.9 1.1 - - + -
140H TYR* 1.3 77.4 - - - +
142H ASN* 1.3 72.6 + - - +
145H ASP* 3.5 30.5 - - + +
146H ALA* 3.8 8.7 - - - -
149H VAL* 3.9 15.9 - - + -
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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