Contacts of the strand formed by residues 130 - 140 (chain F) in PDB entry 4YHP
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 THR 130 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E LYS* 4.5 10.8 - - - +
125F GLN* 3.1 46.6 + - - +
126F LEU* 3.9 5.2 + - - +
128F SER* 3.5 9.2 + - - -
129F GLY* 1.3 83.9 + - - +
131F ALA* 1.3 62.4 + - - +
181F THR* 3.9 21.1 - - + -
182F LEU 3.5 12.8 - - - +
183F SER* 5.4 0.6 - - - -
184F LYS* 4.0 4.3 - - - +
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Residues in contact with ALA 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F PRO* 3.9 15.5 - - + -
125F GLN* 4.0 2.2 - - - -
126F LEU* 3.9 6.7 - - + -
130F THR* 1.3 74.8 - - - +
132F SER* 1.3 61.4 + - - +
133F VAL* 4.9 2.5 - - + +
180F LEU 3.4 1.7 - - - +
181F THR* 3.4 2.9 - - - -
182F LEU* 2.8 44.0 + - + +
183F SER 4.3 1.3 - - - +
187F TYR* 3.7 39.3 - - + -
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Residues in contact with SER 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU* 5.8 2.6 - - - +
149E LEU* 3.8 18.3 - - - +
151E LYS* 3.3 19.1 - - - -
119F PHE 4.3 0.2 - - - +
120F PRO 4.2 1.9 - - - +
121F PRO* 3.5 21.6 - - - +
125F GLN* 3.0 33.2 + - - +
131F ALA* 1.3 73.5 - - - +
133F VAL* 1.3 61.7 + - - +
134F VAL* 4.2 4.0 + - - +
179F THR* 4.0 13.7 - - - +
180F LEU 3.3 4.0 - - - -
181F THR* 3.8 9.9 + - - +
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Residues in contact with VAL 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ILE* 4.3 2.5 - - + -
119F PHE 3.5 13.5 - - - +
121F PRO* 3.9 17.5 - - + -
131F ALA* 4.9 3.4 - - + +
132F SER* 1.3 76.3 - - - +
134F VAL* 1.3 63.7 + - - +
149F TRP* 3.5 25.1 - - + -
179F THR* 3.2 3.1 - - - -
180F LEU* 2.6 58.3 + - + +
182F LEU* 5.9 2.2 - - + -
187F TYR* 4.6 6.3 - - + -
193F TYR* 4.4 20.9 - - + -
210F PHE* 3.6 20.6 - - + -
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Residues in contact with VAL 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E LEU* 4.2 26.9 - - + -
149E LEU* 4.8 5.4 - - + -
187E SER* 4.3 13.5 - - - +
189E VAL* 5.8 1.8 - - + -
118F ILE* 3.4 4.3 - - - +
119F PHE* 2.8 57.1 + - + -
132F SER* 4.9 4.3 - - - +
133F VAL* 1.3 81.6 - - - +
135F CYS* 1.3 70.5 + - - +
136F LEU* 4.6 2.5 - - + +
149F TRP* 3.9 3.6 - - - -
177F SER* 4.8 11.0 - - - -
178F SER 3.3 4.3 - - - +
179F THR* 3.8 24.0 - - + +
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Residues in contact with CYS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F VAL* 3.8 15.7 - - - -
117F PHE 3.3 2.9 - - - -
118F ILE* 4.5 0.2 - - - +
134F VAL* 1.3 74.7 - - - +
136F LEU* 1.3 62.5 + - - +
137F LEU* 4.2 12.3 - - + +
147F VAL* 5.1 1.8 - - + -
149F TRP* 3.5 18.1 - - + -
176F LEU 3.9 0.3 - - - +
177F SER* 3.3 6.1 - - - -
178F SER* 2.8 42.9 + - - +
195F CYS* 2.0 50.3 - - + -
197F VAL* 4.3 2.9 - - - -
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Residues in contact with LEU 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145E ALA* 3.9 17.3 - - + -
174E PHE* 3.7 22.9 - - + -
189E VAL* 3.9 31.2 - - + -
191E THR* 5.1 1.6 - - + -
115F SER 3.3 1.6 - - - +
116F VAL* 3.2 9.2 - - - +
117F PHE* 2.6 65.7 + - + +
119F PHE* 4.0 10.5 - - + -
134F VAL* 4.1 3.3 + - + -
135F CYS* 1.3 73.6 - - - +
137F LEU* 1.3 75.7 + - - +
138F ASN* 4.4 14.8 - - + +
175F SER* 5.1 0.4 - - - -
176F LEU 3.7 9.0 - - - +
177F SER* 4.8 1.1 - - - +
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Residues in contact with LEU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F PRO* 4.2 9.9 - - + -
115F SER 3.5 3.6 - - - -
116F VAL* 4.6 1.8 - - + -
135F CYS* 4.2 11.0 - - - +
136F LEU* 1.3 78.7 - - - +
138F ASN* 1.3 59.2 + - - +
140F PHE* 3.5 22.0 - - + -
145F ALA* 3.8 25.8 - - + -
147F VAL* 3.9 24.0 - - + -
175F SER* 3.3 7.3 - - - -
176F LEU* 2.8 50.0 + - + +
197F VAL* 3.7 45.8 - - + -
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Residues in contact with ASN 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E GLY 5.0 0.2 - - - +
172E HIS* 3.1 27.6 + - - -
189E VAL* 5.0 1.0 - - - +
191E THR* 3.7 30.5 + - - +
113F ALA 4.5 0.3 - - - +
114F PRO* 3.5 2.0 - - - +
115F SER* 2.7 49.7 + - - +
117F PHE* 4.4 7.9 - - + -
136F LEU* 4.4 12.9 - - + +
137F LEU* 1.3 72.3 - - - +
139F ASN* 1.3 93.3 + - - +
140F PHE* 3.7 1.8 - - - -
175F SER* 3.7 0.6 + - - -
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Residues in contact with ASN 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A PRO* 5.1 7.7 - - - +
195A SER* 3.4 21.3 + - - +
170E GLY* 6.2 1.2 - - - -
172E HIS* 2.6 34.1 + - - -
112F ALA* 4.0 2.8 - - - +
113F ALA 4.0 8.3 - - - +
138F ASN* 1.3 89.9 + - - +
140F PHE* 1.3 59.8 + - - +
168F ASP* 5.4 2.2 + - - -
171F ASP* 3.1 22.0 + - - -
173F THR* 3.4 23.2 + - - +
174F TYR 3.3 6.8 + - - -
175F SER* 3.0 9.3 + - - -
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Residues in contact with PHE 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112F ALA* 3.2 14.4 - - - +
114F PRO* 3.6 34.8 - - + -
137F LEU* 3.5 35.9 - - + -
139F ASN* 1.3 74.3 - - - +
141F TYR* 1.3 63.8 + - - +
142F PRO 3.2 19.5 - - - -
143F ARG* 3.4 30.5 - - - -
145F ALA* 4.1 10.1 - - + -
164F VAL* 5.2 1.3 - - + -
173F THR* 3.4 3.6 - - - -
174F TYR* 2.8 60.1 + - + +
175F SER 4.3 2.2 - - - -
176F LEU* 3.6 25.4 - - + -
199F HIS* 3.8 9.4 - + - +
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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