Contacts of the strand formed by residues 109 - 115 (chain A) in PDB entry 1ULH
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 PHE 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A VAL* 3.5 34.5 - - + +
102A ALA* 5.7 1.6 - - + -
103A TYR* 3.9 19.1 - + + -
107A LYS 5.0 1.1 - - - +
108A PRO* 1.3 78.5 - - - +
110A TYR* 1.3 73.0 + - - +
111A LEU* 4.4 6.3 - - + -
136A LEU* 5.4 0.2 - - + -
140A PHE* 3.5 49.8 - + + -
142A VAL* 3.3 48.2 - - + +
143A PRO* 3.7 4.9 - - - +
256A ILE* 3.8 6.2 - - - +
257A GLN* 3.4 21.1 - - + +
259A LEU* 3.6 33.2 - - + -
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Residues in contact with TYR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 1.3 80.1 - - - +
111A LEU* 1.3 77.9 + - - +
112A TYR* 4.4 2.9 - - + -
142A VAL* 4.5 1.1 - - - -
143A PRO* 3.6 13.9 - - + +
145A VAL* 4.6 11.2 - - + -
240A PRO 2.6 29.6 + - - -
241A SER 3.0 14.8 - - - -
242A PHE 3.1 1.2 + - - -
243A SER* 3.1 26.2 + - - -
246A PHE* 4.5 2.5 - + - -
250A PHE* 3.4 35.0 - + + -
256A ILE* 3.4 30.5 - - + -
257A GLN 2.9 24.5 + - - -
258A CYS* 3.3 24.3 - - + -
259A LEU* 2.7 31.5 + - - -
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PHE* 4.4 1.6 - - + -
110A TYR* 1.3 88.4 - - - +
112A TYR* 1.3 62.0 + - - +
133A THR* 3.8 12.8 - - + +
136A LEU* 3.7 31.9 - - + -
137A GLN* 3.6 38.4 - - + +
142A VAL* 4.0 15.5 - - + -
143A PRO 2.9 11.4 + - - +
144A LEU* 3.4 16.1 - - + -
145A VAL 3.0 20.3 + - - -
259A LEU* 3.3 33.7 - - + +
261A PRO* 4.1 6.1 - - + -
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Residues in contact with TYR 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A TYR* 4.4 2.2 - - + -
111A LEU* 1.3 79.3 - - - +
113A THR* 1.3 85.1 + - - +
114A GLY* 4.2 7.4 + - - -
144A LEU* 4.1 1.6 - - - -
145A VAL* 3.4 21.5 - - + +
147A GLN* 3.7 29.8 + - + -
237A GLN* 3.8 21.9 + - - +
240A PRO* 3.5 30.1 - - + -
241A SER* 4.8 2.9 - - - -
258A CYS* 3.7 20.2 - - - -
259A LEU 3.1 5.1 + - - -
260A ILE* 3.5 35.8 - - + +
261A PRO* 3.5 16.5 - - - +
270A PHE* 4.1 19.0 - + - -
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Residues in contact with THR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR* 1.3 90.6 - - - +
114A GLY* 1.3 70.3 + - - +
129A PRO* 4.8 9.5 - - - +
130A PHE* 3.9 27.8 - - + -
133A THR* 4.3 20.4 - - + +
144A LEU* 4.3 13.5 - - + -
145A VAL 3.1 8.4 + - - +
146A ILE* 3.2 10.3 - - + -
147A GLN 2.9 18.7 + - - -
260A ILE* 5.4 0.9 - - - -
261A PRO* 4.1 14.3 + - - -
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Residues in contact with GLY 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A TYR* 4.2 8.2 + - - -
113A THR* 1.3 85.3 + - - +
115A ARG* 1.3 64.2 + - - +
130A PHE* 3.8 11.5 - - - -
146A ILE* 4.4 2.0 - - - -
147A GLN* 3.1 20.4 - - - -
149A THR* 6.1 0.4 - - - -
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Residues in contact with ARG 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A GLY* 1.3 75.7 - - - +
116A GLY* 1.3 73.0 + - - +
117A PRO* 3.0 15.1 - - - +
118A SER 4.8 8.1 + - - -
120A GLU* 5.0 3.0 - - - +
121A ALA 5.5 0.2 - - - -
122A MET* 3.1 42.3 - - - +
126A HIS* 3.0 46.4 + - - +
130A PHE* 4.1 7.9 - - + -
147A GLN 2.6 8.5 + - - +
148A MET* 3.4 27.1 - - + -
149A THR* 3.1 17.1 + - - +
171A ASN* 2.8 26.5 - - - +
175A ILE* 4.0 11.7 - - + -
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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